diff --git a/backend/package/yuxi/agents/backends/knowledge_base_backend.py b/backend/package/yuxi/agents/backends/knowledge_base_backend.py
index 729a942d..0d08f6a1 100644
--- a/backend/package/yuxi/agents/backends/knowledge_base_backend.py
+++ b/backend/package/yuxi/agents/backends/knowledge_base_backend.py
@@ -127,11 +127,6 @@ async def resolve_visible_knowledge_bases_for_context(context) -> list[dict[str,
         setattr(context, "_visible_knowledge_bases", [])
         return []
 
-    enabled_names = {str(name).strip() for name in (getattr(context, "knowledges", None) or []) if str(name).strip()}
-    if not enabled_names:
-        setattr(context, "_visible_knowledge_bases", [])
-        return []
-
     try:
         raw_user_id = int(user_id)
     except (TypeError, ValueError):
@@ -139,7 +134,12 @@ async def resolve_visible_knowledge_bases_for_context(context) -> list[dict[str,
         return []
 
     result = await knowledge_base.get_databases_by_raw_id(raw_user_id)
-    databases = [db for db in (result.get("databases") or []) if str(db.get("name") or "").strip() in enabled_names]
+    databases = result.get("databases") or []
+    enabled_knowledges = getattr(context, "knowledges", None)
+    if enabled_knowledges is not None:
+        enabled_names = {str(name).strip() for name in enabled_knowledges if str(name).strip()}
+        databases = [db for db in databases if str(db.get("name") or "").strip() in enabled_names]
+
     setattr(context, "_visible_knowledge_bases", databases)
     return databases
 
diff --git a/backend/package/yuxi/agents/context.py b/backend/package/yuxi/agents/context.py
index 4009fa03..851780b6 100644
--- a/backend/package/yuxi/agents/context.py
+++ b/backend/package/yuxi/agents/context.py
@@ -55,11 +55,11 @@ class BaseContext:
         },
     )
 
-    knowledges: Annotated[list[str], {"__template_metadata__": {"kind": "knowledges"}}] = field(
-        default_factory=list,
+    knowledges: Annotated[list[str] | None, {"__template_metadata__": {"kind": "knowledges"}}] = field(
+        default=None,
         metadata={
             "name": "知识库",
-            "description": "知识库列表，可以在左侧知识库页面中创建知识库。",
+            "description": "知识库列表，可以在左侧知识库页面中创建知识库。默认选择当前用户可访问的全部知识库。",
             "type": "list",  # Explicitly mark as list type for frontend if needed
         },
     )
diff --git a/backend/package/yuxi/agents/toolkits/kbs/tools.py b/backend/package/yuxi/agents/toolkits/kbs/tools.py
index 62daa0af..e572ba4e 100644
--- a/backend/package/yuxi/agents/toolkits/kbs/tools.py
+++ b/backend/package/yuxi/agents/toolkits/kbs/tools.py
@@ -39,8 +39,7 @@ async def list_kbs(dummy: str, runtime: ToolRuntime) -> str:  # Now has 2 params
     # 打印 runtime—context 中的所有信息以进行调试
     logger.debug(f"Runtime context: {runtime_context.__dict__}")
 
-    # 获取用户在当前对话中启用的知识库列表
-    enabled_kb_names = getattr(runtime_context, "knowledges", []) or []
+    enabled_kb_names = getattr(runtime_context, "knowledges", None)
 
     # 获取用户可访问的知识库列表（包含名称和描述）
     try:
@@ -55,8 +54,10 @@ async def list_kbs(dummy: str, runtime: ToolRuntime) -> str:  # Now has 2 params
     logger.debug(f"用户 {user_id} 可访问的知识库列表: {all_kb_names}")
     logger.debug(f"用户 {user_id} 当前对话启用的知识库列表: {enabled_kb_names}")
 
-    # 与启用的知识库取交集
-    available_kbs = [kb for kb in all_kbs if kb["name"] in enabled_kb_names]
+    if enabled_kb_names is None:
+        available_kbs = all_kbs
+    else:
+        available_kbs = [kb for kb in all_kbs if kb["name"] in enabled_kb_names]
 
     if not available_kbs:
         return "当前没有可访问的知识库"
diff --git a/docs/develop-guides/roadmap.md b/docs/develop-guides/roadmap.md
index 59b8442d..1eb7cad8 100644
--- a/docs/develop-guides/roadmap.md
+++ b/docs/develop-guides/roadmap.md
@@ -19,7 +19,6 @@
     - 前置任务，多知识库并行检索（扩展 query_kb）
     - 新增 query_keywords 工具，专门用于基于关键词命中的排序，也结合词频（和 BM25 的区别？）
 - 评估，基于 Agent 的评估，这里应该是结合 Langfuse 实现
-- 知识库选择，修改为默认选择所有知识库（dev2）
 
 ### Bugs
 - 目前的知识库的图片存在公开访问风险
@@ -37,6 +36,7 @@
 ### 0.6.2 开发记录
 
 <!-- 0.6.2 的内容请放在这里 -->
+- 调整 Agent 知识库默认选择：未显式配置知识库时默认启用当前用户可访问的全部知识库，显式保存空列表仍表示不启用知识库。
 - 优化评估基准自动生成：仅支持 commonrag/Milvus 知识库，默认参考 chunks 数量改为 1；多 chunk 场景复用知识库向量检索选择相似 chunks，不再对全量 chunks 重新计算 embedding，并移除前端 Embedding 模型选择。
 - 修复知识库文档入库状态回退：当已解析文件缺失 `markdown_file` 解析产物时，索引流程会将文件状态恢复为未解析，便于重新解析而不是停留在索引失败。
 - 优化 Agent 输入框文件 mention：用户级 workspace 文件候选改为从独立 workspace API 递归加载，不再依赖 active thread；插入时仍转换为 `/home/gem/user-data/workspace/` 沙盒虚拟路径，并修复附件上传后未立即刷新 mention 候选的问题。
diff --git a/web/src/components/AgentConfigSidebar.vue b/web/src/components/AgentConfigSidebar.vue
index fcf8f6df..dcf1a53f 100644
--- a/web/src/components/AgentConfigSidebar.vue
+++ b/web/src/components/AgentConfigSidebar.vue
@@ -824,6 +824,9 @@ const handleModelChange = (key, spec) => {
 // 多选相关方法
 const ensureArray = (key) => {
   const config = agentConfig.value || {}
+  if (config[key] === null && configurableItems.value[key]?.template_metadata?.kind === 'knowledges') {
+    return getConfigOptions(configurableItems.value[key]).map((option) => getOptionValue(option))
+  }
   if (!config[key] || !Array.isArray(config[key])) {
     return []
   }
@@ -891,8 +894,7 @@ const openSelectionModal = async (key) => {
   if (configurableItems.value[key]?.template_metadata?.kind === 'subagents') {
     await loadSubagentOptions()
   }
-  const currentValues = agentConfig.value[key] || []
-  tempSelectedValues.value = [...currentValues]
+  tempSelectedValues.value = [...ensureArray(key)]
   selectionModalOpen.value = true
 }
 
diff --git a/web/src/composables/useAgentMentionConfig.js b/web/src/composables/useAgentMentionConfig.js
index 3ce5442e..6db965fe 100644
--- a/web/src/composables/useAgentMentionConfig.js
+++ b/web/src/composables/useAgentMentionConfig.js
@@ -91,6 +91,7 @@ export function useAgentMentionConfig({
 
     const configItems = configurableItems.value || {}
     const currentConfig = agentConfig.value || {}
+    let includeAllKnowledgeBases = false
     const allowedKbNames = new Set()
     const allowedMcpNames = new Set()
     const allowedSkillNames = new Set()
@@ -101,7 +102,9 @@ export function useAgentMentionConfig({
       const kind = item?.template_metadata?.kind
       const val = currentConfig[key]
 
-      if (Array.isArray(val)) {
+      if (kind === 'knowledges' && val === null) {
+        includeAllKnowledgeBases = true
+      } else if (Array.isArray(val)) {
         if (kind === 'knowledges') {
           val.forEach((v) => allowedKbNames.add(v))
         } else if (kind === 'mcps') {
@@ -133,7 +136,9 @@ export function useAgentMentionConfig({
       }
     })
 
-    const knowledgeBases = availableKnowledgeBases.value.filter((kb) => allowedKbNames.has(kb.name))
+    const knowledgeBases = includeAllKnowledgeBases
+      ? availableKnowledgeBases.value
+      : availableKnowledgeBases.value.filter((kb) => allowedKbNames.has(kb.name))
     const mcps = availableMcps.value.filter((mcp) => allowedMcpNames.has(mcp.name))
     const skills = availableSkills.value.filter((skill) => {
       const skillName = skill.name || ''