diff --git a/backend/package/yuxi/agents/buildin/chatbot/graph.py b/backend/package/yuxi/agents/buildin/chatbot/graph.py
index cfa83a33..706d75c7 100644
--- a/backend/package/yuxi/agents/buildin/chatbot/graph.py
+++ b/backend/package/yuxi/agents/buildin/chatbot/graph.py
@@ -30,28 +30,35 @@ class ChatbotAgent(BaseAgent):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
-    async def get_graph(self, **kwargs):
-        """构建图"""
-        context = self.context_schema()
+    async def _build_middlewares(self, context):
+        """构建中间件列表"""
         all_mcp_tools = (
             await get_tools_from_all_servers()
         )  # 因为异步加载，无法放在 RuntimeConfigMiddleware 的 __init__ 中
 
+        middlewares = [
+            save_attachments_to_fs,  # 附件注入提示词
+            FilesystemMiddleware(backend=_create_fs_backend),  # 文件系统后端
+            KnowledgeBaseMiddleware(),  # 知识库工具
+            RuntimeConfigMiddleware(extra_tools=all_mcp_tools),  # 运行时配置应用（模型/工具/MCP/提示词）
+            SkillsMiddleware(),  # Skills 中间件（提示词注入、依赖展开、动态激活）
+            ModelRetryMiddleware(),  # 模型重试中间件
+            TodoListMiddleware(),
+            PatchToolCallsMiddleware(),
+        ]
+
+        return middlewares
+
+    async def get_graph(self, context=None, **kwargs):
+
+        context = context or self.context_schema()  # 获取上下文配置
+
         # 使用 create_agent 创建智能体
         # 注意：tools 参数由 RuntimeConfigMiddleware 在 wrap_model_call 中动态设置
         graph = create_agent(
             model=load_chat_model(fully_specified_name=context.model),
             system_prompt=context.system_prompt,
-            middleware=[
-                save_attachments_to_fs,  # 附件注入提示词
-                FilesystemMiddleware(backend=_create_fs_backend),  # 文件系统后端
-                KnowledgeBaseMiddleware(),  # 知识库工具
-                RuntimeConfigMiddleware(extra_tools=all_mcp_tools),  # 运行时配置应用（模型/工具/MCP/提示词）
-                SkillsMiddleware(),  # Skills 中间件（提示词注入、依赖展开、动态激活）
-                ModelRetryMiddleware(),  # 模型重试中间件
-                TodoListMiddleware(),
-                PatchToolCallsMiddleware(),
-            ],
+            middleware=await self._build_middlewares(context),
             checkpointer=await self._get_checkpointer(),
         )
 
diff --git a/backend/package/yuxi/agents/buildin/deep_agent/graph.py b/backend/package/yuxi/agents/buildin/deep_agent/graph.py
index 67a42aa4..c4213916 100644
--- a/backend/package/yuxi/agents/buildin/deep_agent/graph.py
+++ b/backend/package/yuxi/agents/buildin/deep_agent/graph.py
@@ -56,10 +56,9 @@ class DeepAgent(BaseAgent):
             logger.warning("No search tools configured, DeepAgent will work without web search")
         return tools
 
-    async def get_graph(self, **kwargs):
-        """构建 Deep Agent 的图"""
-        # 获取上下文配置
-        context = self.context_schema.from_file(module_name=self.module_name)
+    async def get_graph(self, context=None, **kwargs):
+
+        context = context or self.context_schema()  # 获取上下文配置
 
         model = load_chat_model(context.model)
         sub_model = load_chat_model(context.subagents_model)
diff --git a/backend/package/yuxi/agents/buildin/reporter/graph.py b/backend/package/yuxi/agents/buildin/reporter/graph.py
index bd8ddc4a..4ca44ef2 100644
--- a/backend/package/yuxi/agents/buildin/reporter/graph.py
+++ b/backend/package/yuxi/agents/buildin/reporter/graph.py
@@ -69,9 +69,10 @@ class SqlReporterAgent(BaseAgent):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
-    async def get_graph(self, **kwargs):
-        """构建图"""
-        context = self.context_schema.from_file(module_name=self.module_name)
+    async def get_graph(self, context=None, **kwargs):
+
+        context = context or self.context_schema()  # 获取上下文配置
+
         all_mcp_tools = await get_tools_from_all_servers()
 
         graph = create_agent(
diff --git a/backend/package/yuxi/agents/common/base.py b/backend/package/yuxi/agents/common/base.py
index bc7f1094..8788f25b 100644
--- a/backend/package/yuxi/agents/common/base.py
+++ b/backend/package/yuxi/agents/common/base.py
@@ -65,26 +65,20 @@ class BaseAgent:
         }
 
     async def get_config(self):
-        return self.context_schema.from_file(module_name=self.module_name)
+        return self.context_schema()
 
     async def stream_values(self, messages: list[str], input_context=None, **kwargs):
-        graph = await self.get_graph()
         context = self.context_schema()
-        agent_config = (input_context or {}).get("agent_config")
-        if isinstance(agent_config, dict):
-            context.update(agent_config)
-        context.update(input_context or {})
+        context.update_from_dict(input_context or {})
+        graph = await self.get_graph(context=context)
         for event in graph.astream({"messages": messages}, stream_mode="values", context=context):
             yield event["messages"]
 
     async def stream_messages(self, messages: list[str], input_context=None, **kwargs):
-        graph = await self.get_graph()
         context = self.context_schema()
-        agent_config = (input_context or {}).get("agent_config")
-        if isinstance(agent_config, dict):
-            context.update(agent_config)
-        context.update(input_context or {})
-        logger.debug(f"stream_messages: {context}")
+        context.update_from_dict(input_context or {})
+        graph = await self.get_graph(context=context)
+        logger.debug(f"stream_messages: {context=}")
 
         # 构建配置：LangGraph 会自动从 checkpointer 恢复 state
         input_config = {
@@ -101,12 +95,9 @@ class BaseAgent:
             yield msg, metadata
 
     async def invoke_messages(self, messages: list[str], input_context=None, **kwargs):
-        graph = await self.get_graph()
         context = self.context_schema()
-        agent_config = (input_context or {}).get("agent_config")
-        if isinstance(agent_config, dict):
-            context.update(agent_config)
-        context.update(input_context or {})
+        context.update_from_dict(input_context or {})
+        graph = await self.get_graph(context=context)
         logger.debug(f"invoke_messages: {context}")
 
         # 构建配置
diff --git a/backend/package/yuxi/agents/common/context.py b/backend/package/yuxi/agents/common/context.py
index d3210ba5..98d4e64c 100644
--- a/backend/package/yuxi/agents/common/context.py
+++ b/backend/package/yuxi/agents/common/context.py
@@ -1,16 +1,11 @@
 """Define the configurable parameters for the agent."""
 
-import os
 import uuid
 from dataclasses import MISSING, dataclass, field, fields
-from pathlib import Path
 from typing import Annotated, get_args, get_origin
 
-import yaml
-
 from yuxi import config as sys_config
 from yuxi.services.mcp_service import get_mcp_server_names
-from yuxi.utils import logger
 
 
 @dataclass(kw_only=True)
@@ -20,8 +15,7 @@ class BaseContext:
 
     配置优先级:
     1. 运行时配置(RunnableConfig)：最高优先级，直接从函数参数传入
-    2. 文件配置(config.private.yaml)：中等优先级，从文件加载
-    3. 类默认配置：最低优先级，类中定义的默认值
+    2. 类默认配置：最低优先级，类中定义的默认值
     """
 
     def update(self, data: dict):
@@ -40,10 +34,11 @@ class BaseContext:
         metadata={"name": "用户ID", "configurable": False, "description": "用来唯一标识一个用户"},
     )
 
-    department_id: int | None = field(
-        default=None,
-        metadata={"name": "部门ID", "configurable": False, "description": "用来唯一标识一个部门"},
-    )
+    # 不需要了，使用 user_id 判断
+    # department_id: int | None = field(
+    #     default=None,
+    #     metadata={"name": "部门ID", "configurable": False, "description": "用来唯一标识一个部门"},
+    # )
 
     system_prompt: Annotated[str, {"__template_metadata__": {"kind": "prompt"}}] = field(
         default="You are a helpful assistant.",
@@ -99,50 +94,6 @@ class BaseContext:
         },
     )
 
-    @classmethod
-    def from_file(cls, module_name: str, input_context: dict = None) -> "BaseContext":
-        """Load configuration from a YAML file. 用于持久化配置"""
-
-        # 从文件加载配置
-        context = cls()
-        config_file_path = Path(sys_config.save_dir) / "agents" / module_name / "config.yaml"
-        if module_name is not None and os.path.exists(config_file_path):
-            file_config = {}
-            try:
-                with open(config_file_path, encoding="utf-8") as f:
-                    file_config = yaml.safe_load(f) or {}
-            except Exception as e:
-                logger.error(f"加载智能体配置文件出错: {e}")
-
-            context.update(file_config)
-
-        if input_context:
-            context.update(input_context)
-
-        return context
-
-    @classmethod
-    def save_to_file(cls, config: dict, module_name: str) -> bool:
-        """Save configuration to a YAML file 用于持久化配置"""
-
-        configurable_items = cls.get_configurable_items()
-        configurable_config = {}
-        for k, v in config.items():
-            if k in configurable_items:
-                configurable_config[k] = v
-
-        try:
-            config_file_path = Path(sys_config.save_dir) / "agents" / module_name / "config.yaml"
-            # 确保目录存在
-            os.makedirs(os.path.dirname(config_file_path), exist_ok=True)
-            with open(config_file_path, "w", encoding="utf-8") as f:
-                yaml.dump(configurable_config, f, indent=2, allow_unicode=True)
-
-            return True
-        except Exception as e:
-            logger.error(f"保存智能体配置文件出错: {e}")
-            return False
-
     @classmethod
     def get_configurable_items(cls):
         """实现一个可配置的参数列表，在 UI 上配置时使用"""
@@ -210,3 +161,9 @@ class BaseContext:
                         if isinstance(metadata, dict) and "__template_metadata__" in metadata:
                             return metadata["__template_metadata__"]
         return {}
+
+    def update_from_dict(self, data: dict):
+        """从字典更新配置字段"""
+        for key, value in data.items():
+            if hasattr(self, key):
+                setattr(self, key, value)
diff --git a/backend/package/yuxi/agents/common/middlewares/runtime_config_middleware.py b/backend/package/yuxi/agents/common/middlewares/runtime_config_middleware.py
index 63780cdc..455256a5 100644
--- a/backend/package/yuxi/agents/common/middlewares/runtime_config_middleware.py
+++ b/backend/package/yuxi/agents/common/middlewares/runtime_config_middleware.py
@@ -72,17 +72,6 @@ class RuntimeConfigMiddleware(AgentMiddleware):
                 "将忽略 extra_tools 并不会应用任何工具覆盖。"
             )
 
-        logger.debug(
-            f"Initialized RuntimeConfigMiddleware with custom field names: model={model_context_name}, "
-            f"system_prompt={system_prompt_context_name}, tools={tools_context_name}, "
-            f"knowledges={knowledges_context_name}, mcps={mcps_context_name}"
-        )
-
-    async def abefore_agent(self, state, runtime) -> dict[str, Any] | None:
-        # abefore_agent 在 RuntimeConfigMiddleware 中暂无额外逻辑
-        # Skills 相关逻辑已移至 SkillsMiddleware
-        return None
-
     async def awrap_model_call(
         self, request: ModelRequest, handler: Callable[[ModelRequest], ModelResponse]
     ) -> ModelResponse:
diff --git a/backend/package/yuxi/services/chat_stream_service.py b/backend/package/yuxi/services/chat_stream_service.py
index 382c8f06..62ff7fdf 100644
--- a/backend/package/yuxi/services/chat_stream_service.py
+++ b/backend/package/yuxi/services/chat_stream_service.py
@@ -14,6 +14,7 @@ from yuxi.plugins.guard import content_guard
 from yuxi.repositories.agent_config_repository import AgentConfigRepository
 from yuxi.repositories.conversation_repository import ConversationRepository
 from yuxi.storage.postgres.manager import pg_manager
+from yuxi.storage.postgres.models_business import User
 from yuxi.utils.logging_config import logger
 from yuxi.utils.question_utils import (
     normalize_options as _normalize_interrupt_options,
@@ -297,28 +298,23 @@ def _ensure_full_msg(full_msg: AIMessage | None, accumulated_content: list[str])
     return full_msg
 
 
-async def _resolve_agent_config(
-    db, agent_id: str, department_id, user_id: str, agent_config_id: int | str | None
-) -> tuple:
-    """解析 agent_config，返回 (config_item, agent_config_id)"""
-    config_repo = AgentConfigRepository(db)
+async def _resolve_agent_config(db, agent_id: str, user: User, agent_config_id):
+    """解析 agent_config，返回 agent_config"""
+    department_id = user.department_id
+
+    agent_config_repo = AgentConfigRepository(db)
     config_item = None
     if agent_config_id is not None:
-        try:
-            config_item = await config_repo.get_by_id(int(agent_config_id))
-        except Exception:
-            logger.warning(f"Failed to fetch agent config {agent_config_id}: {traceback.format_exc()}")
-            config_item = None
+        config_item = await agent_config_repo.get_by_id(config_id=int(agent_config_id))
         if config_item is not None and (config_item.department_id != department_id or config_item.agent_id != agent_id):
             config_item = None
 
     if config_item is None:
-        config_item = await config_repo.get_or_create_default(
-            department_id=department_id, agent_id=agent_id, created_by=user_id
+        config_item = await agent_config_repo.get_or_create_default(
+            department_id=department_id, agent_id=agent_id, created_by=str(user.id)
         )
-        agent_config_id = config_item.id
 
-    return config_item, agent_config_id
+    return (config_item.config_json or {}).get("context", {})
 
 
 async def check_and_handle_interrupts(
@@ -408,26 +404,14 @@ async def stream_agent_chat(
     messages = [human_message]
 
     user_id = str(current_user.id)
-    department_id = current_user.department_id
-    if not department_id:
-        yield make_chunk(status="error", error_type="no_department", error_message="当前用户未绑定部门", meta=meta)
-        return
-
     agent_config_id = config.get("agent_config_id")
-    config_item, agent_config_id = await _resolve_agent_config(db, agent_id, department_id, user_id, agent_config_id)
+    agent_config = await _resolve_agent_config(db, agent_id, current_user, agent_config_id)
 
     if not (thread_id := config.get("thread_id")):
         thread_id = str(uuid.uuid4())
         logger.warning(f"No thread_id provided, generated new thread_id: {thread_id}")
 
-    agent_config = (config_item.config_json or {}).get("context", {})
-    input_context = {
-        "user_id": user_id,
-        "thread_id": thread_id,
-        "department_id": department_id,
-        "agent_config_id": agent_config_id,
-        "agent_config": agent_config,
-    }
+    input_context = agent_config | {"user_id": user_id, "thread_id": thread_id}
     full_msg = None
     accumulated_content: list[str] = []
 
@@ -595,28 +579,12 @@ async def stream_agent_resume(
     graph = await agent.get_graph()
 
     user_id = str(current_user.id)
-    department_id = current_user.department_id
-    if not department_id:
-        yield make_resume_chunk(
-            status="error", error_type="no_department", error_message="当前用户未绑定部门", meta=meta
-        )
-        return
-
     agent_config_id = (config or {}).get("agent_config_id")
-    config_item, agent_config_id = await _resolve_agent_config(db, agent_id, department_id, user_id, agent_config_id)
+    agent_config = await _resolve_agent_config(db, agent_id, current_user, agent_config_id)
 
-    input_context = {
-        "user_id": user_id,
-        "thread_id": thread_id,
-        "department_id": department_id,
-        "agent_config_id": agent_config_id,
-        "agent_config": (config_item.config_json or {}).get("context", config_item.config_json or {}),
-    }
     context = agent.context_schema()
-    agent_config = input_context.get("agent_config")
-    if isinstance(agent_config, dict):
-        context.update(agent_config)
-    context.update(input_context)
+    context.update(agent_config or {})
+    context.update({"user_id": user_id, "thread_id": thread_id})
 
     stream_source = graph.astream(
         resume_command,
diff --git a/backend/server/routers/chat_router.py b/backend/server/routers/chat_router.py
index c8271cbe..c6a7fd8b 100644
--- a/backend/server/routers/chat_router.py
+++ b/backend/server/routers/chat_router.py
@@ -593,64 +593,6 @@ async def resume_agent_chat(
     )
 
 
-@chat.post("/agent/{agent_id}/config")
-async def save_agent_config(
-    agent_id: str,
-    config: dict = Body(...),
-    reload_graph: bool = Query(True),
-    current_user: User = Depends(get_required_user),
-):
-    """保存智能体配置到YAML文件（需要登录）"""
-    try:
-        # 获取Agent实例和配置类
-        if not (agent := agent_manager.get_agent(agent_id)):
-            raise HTTPException(status_code=404, detail=f"智能体 {agent_id} 不存在")
-
-        # === 校验知识库权限 ===
-        from yuxi import knowledge_base
-
-        if "knowledges" in config and config["knowledges"]:
-            # 获取用户有权访问的知识库名称
-            try:
-                accessible_databases = await knowledge_base.get_databases_by_user_id(current_user.user_id)
-                accessible_kb_names = {
-                    db.get("name") for db in accessible_databases.get("databases", []) if db.get("name")
-                }
-            except Exception as db_error:
-                logger.warning(f"获取知识库列表失败: {db_error}")
-                # 如果获取失败，superadmin 可以访问所有，非 superadmin 无法访问任何
-                if current_user.role != "superadmin":
-                    raise HTTPException(status_code=500, detail="无法获取知识库列表")
-                # 回退：获取所有数据库名称
-                from yuxi.repositories.knowledge_base_repository import KnowledgeBaseRepository
-
-                kb_repo = KnowledgeBaseRepository()
-                rows = await kb_repo.get_all()
-                accessible_kb_names = {row.name for row in rows if row.name}
-
-            # 检查配置中的知识库是否都可用
-            invalid_kbs = [kb for kb in config["knowledges"] if kb not in accessible_kb_names]
-            if invalid_kbs:
-                raise HTTPException(status_code=403, detail=f"无权访问以下知识库: {', '.join(invalid_kbs)}")
-        # === 校验结束 ===
-
-        # 使用配置类的save_to_file方法保存配置
-        result = agent.context_schema.save_to_file(config, agent.module_name)
-
-        if result:
-            if reload_graph:
-                agent_manager.get_agent(agent_id, reload_graph=True)
-            return {"success": True, "message": f"智能体 {agent.name} 配置已保存"}
-        else:
-            raise HTTPException(status_code=500, detail="保存智能体配置失败")
-
-    except HTTPException:
-        raise
-    except Exception as e:
-        logger.error(f"保存智能体配置出错: {e}, {traceback.format_exc()}")
-        raise HTTPException(status_code=500, detail=f"保存智能体配置出错: {str(e)}")
-
-
 @chat.get("/agent/{agent_id}/history")
 async def get_agent_history(
     agent_id: str, thread_id: str, current_user: User = Depends(get_required_user), db: AsyncSession = Depends(get_db)
@@ -691,23 +633,6 @@ async def get_agent_state(
         raise HTTPException(status_code=500, detail=f"获取AgentState出错: {str(e)}")
 
 
-@chat.get("/agent/{agent_id}/config")
-async def get_agent_config(agent_id: str, current_user: User = Depends(get_required_user)):
-    """从YAML文件加载智能体配置（需要登录）"""
-    try:
-        # 检查智能体是否存在
-        if not (agent := agent_manager.get_agent(agent_id)):
-            raise HTTPException(status_code=404, detail=f"智能体 {agent_id} 不存在")
-
-        config = await agent.get_config()
-        logger.debug(f"config: {config}, ContextClass: {agent.context_schema=}")
-        return {"success": True, "config": config}
-
-    except Exception as e:
-        logger.error(f"加载智能体配置出错: {e}, {traceback.format_exc()}")
-        raise HTTPException(status_code=500, detail=f"加载智能体配置出错: {str(e)}")
-
-
 # ==================== 线程管理 API ====================
 
 
diff --git a/web/src/apis/agent_api.js b/web/src/apis/agent_api.js
index c8542349..6ea0087c 100644
--- a/web/src/apis/agent_api.js
+++ b/web/src/apis/agent_api.js
@@ -3,7 +3,6 @@ import {
   apiPost,
   apiDelete,
   apiPut,
-  apiAdminGet,
   apiAdminPost,
   apiAdminDelete,
   apiRequest
@@ -123,28 +122,6 @@ export const agentApi = {
   updateProviderModels: (provider, models) =>
     apiPost(`/api/chat/models/update?model_provider=${provider}`, models),
 
-  /**
-   * 获取智能体配置
-   * @param {string} agentName - 智能体名称
-   * @returns {Promise} - 智能体配置
-   */
-  getAgentConfig: async (agentName) => {
-    return apiAdminGet(`/api/chat/agent/${agentName}/config`)
-  },
-
-  /**
-   * 保存智能体配置
-   * @param {string} agentName - 智能体名称
-   * @param {Object} config - 配置对象
-   * @param {Object} options - 额外参数 (e.g., { reload_graph: true })
-   * @returns {Promise} - 保存结果
-   */
-  saveAgentConfig: async (agentName, config, options = {}) => {
-    const queryParams = new URLSearchParams(options).toString()
-    const url = `/api/chat/agent/${agentName}/config` + (queryParams ? `?${queryParams}` : '')
-    return apiAdminPost(url, config)
-  },
-
   getAgentConfigs: (agentId) => apiGet(`/api/chat/agent/${agentId}/configs`),
 
   getAgentConfigProfile: (agentId, configId) =>