diff --git a/app/agent/runtime.py b/app/agent/runtime.py
index da2896574..0fdfb936b 100644
--- a/app/agent/runtime.py
+++ b/app/agent/runtime.py
@@ -34,6 +34,19 @@ SUBAGENT_SCHEMA_VERSION = 1
 DEFAULT_PERSONA_ID = "default"
 PERSONA_ID_PATTERN = re.compile(r"^[a-z0-9][a-z0-9_-]{0,63}$")
 
+# 这些 ID 曾随旧版内置目录发布；保留迁移清单可在升级时删除旧副本，同时不影响
+# 用户自行创建的其它 ID。内置 ID 视为保留名称，用户定义应使用不同的 ID。
+REMOVED_BUNDLED_SUBAGENT_IDS = frozenset(
+    {
+        "download-diagnostician",
+        "media-researcher",
+        "moviepilot-explorer",
+        "resource-searcher",
+        "subscription-analyst",
+        "system-diagnostician",
+    }
+)
+
 
 def _default_agent_root_dir() -> Path:
     """从组合根设置服务取得 Agent 目录，导入早期保留旧设置回退。"""
@@ -475,7 +488,7 @@ class AgentRuntimeManager:
         return tuple(entries)
 
     def _sync_bundled_defaults(self) -> None:
-        """同步默认运行时文件，并按版本更新内置子代理定义。"""
+        """同步默认运行时文件，并按版本更新或清理内置子代理定义。"""
         if not self.bundled_defaults_dir.exists():
             return
         for path in sorted(self.bundled_defaults_dir.rglob("*")):
@@ -492,6 +505,29 @@ class AgentRuntimeManager:
             target.parent.mkdir(parents=True, exist_ok=True)
             shutil.copy2(path, target)
             logger.info(f"已同步默认 Agent 运行时文件: {target}")
+        self._remove_removed_bundled_subagents()
+
+    def _remove_removed_bundled_subagents(self) -> None:
+        """删除已从内置目录移除的保留子代理，保留其它用户定义。"""
+        bundled_subagents_root = self.bundled_defaults_dir / SUBAGENTS_DIR
+        bundled_ids = (
+            {path.name for path in bundled_subagents_root.iterdir() if path.is_dir()}
+            if bundled_subagents_root.is_dir()
+            else set()
+        )
+
+        for subagent_id in sorted(REMOVED_BUNDLED_SUBAGENT_IDS - bundled_ids):
+            target_dir = self.subagents_dir / subagent_id
+            target_file = target_dir / SUBAGENT_FILE
+            if not target_file.is_file() and not target_file.is_symlink():
+                continue
+            target_file.unlink()
+            try:
+                target_dir.rmdir()
+            except OSError:
+                # 用户可能在保留目录中放置了其它文件，只移除旧的内置定义。
+                pass
+            logger.info(f"已删除废弃的默认 Agent 子代理定义: {target_file}")
 
     @classmethod
     def _should_update_bundled_subagent(
diff --git a/tests/test_agent_subagent_runtime.py b/tests/test_agent_subagent_runtime.py
index a9da212df..9558c0179 100644
--- a/tests/test_agent_subagent_runtime.py
+++ b/tests/test_agent_subagent_runtime.py
@@ -145,6 +145,35 @@ def test_runtime_updates_bundled_subagent_when_version_increases(tmp_path):
     assert "version two" in subagent.text
 
 
+def test_runtime_removes_removed_bundled_subagents_and_keeps_custom_definitions(tmp_path):
+    """内置子代理删除后应清理旧副本，同时保留未知的用户定义。"""
+    defaults_root = tmp_path / "defaults"
+    _write_current_persona(defaults_root)
+    _write_subagent(defaults_root, "general-purpose")
+
+    runtime_root = tmp_path / "agent" / "runtime"
+    _write_subagent(runtime_root, "download-diagnostician")
+    _write_subagent(
+        runtime_root,
+        "custom-reader",
+        description="Custom reader subagent.",
+        body="Only inspect custom media signals.",
+    )
+
+    manager = AgentRuntimeManager(
+        agent_root_dir=tmp_path / "agent",
+        bundled_defaults_dir=defaults_root,
+    )
+    runtime_config = manager.load_runtime_config()
+
+    assert not (runtime_root / "subagents" / "download-diagnostician").exists()
+    assert (runtime_root / "subagents" / "custom-reader" / "SUBAGENT.md").exists()
+    assert [subagent.subagent_id for subagent in runtime_config.available_subagents] == [
+        "custom-reader",
+        "general-purpose",
+    ]
+
+
 def test_middleware_profiles_are_loaded_from_runtime_config(monkeypatch, tmp_path):
     """子代理中间件应从运行时 YAML 定义生成 profile。"""
     defaults_root = tmp_path / "defaults"