diff --git a/docs/cli.md b/docs/cli.md
index a1e06935c..c74b48681 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -27,7 +27,7 @@ curl -fsSL https://raw.githubusercontent.com/jxxghp/MoviePilot/v3/scripts/bootst
 - 如果系统里已经有可用的 `Python 3.14+`，脚本会优先直接复用本地解释器
 - 如果系统里没有可用解释器，脚本会通过最新稳定版 uv 安装 Python 3.14
 - Linux 下安装系统依赖时通常需要 `sudo`
-- 复用已有仓库时，脚本现在只会因为已跟踪源码改动而阻止自动更新，不会再被 `.DS_Store` 之类未跟踪文件卡住
+- 复用已有仓库时，如果检测到已跟踪源码改动，脚本会先询问是否清空本地改动；确认后才会继续更新，拒绝或非交互模式会取消更新，不会删除被 Git 忽略的配置和运行时文件
 
 如果安装完成后当前终端仍提示找不到 `moviepilot`：
 
@@ -357,6 +357,7 @@ moviepilot update all --skip-resources
 说明：
 
 - `update backend` 会更新 Git 仓库并重新安装后端依赖，包括 `moviepilot-rust` 加速扩展
+- 后端更新前如果检测到已跟踪源码改动，CLI 会列出部分文件并询问是否清空；确认后执行清理并继续更新，拒绝或非交互模式会取消更新
 - `MOVIEPILOT_UPDATE_DEV=true` 时，`moviepilot update` 默认使用 DEV 模式；`--dev` / `--no-dev` 可临时覆盖，省略目标时更新全部组件。进程环境变量优先于配置目录中的 `app.env`
 - DEV 模式后端跟踪当前开发分支，处于 Release 的 detached HEAD 时回到 `v3`；前端下载最新 Release 的 `dist.zip`。显式 `--ref` / `--frontend-version` 优先于默认选择
 - DEV 模式每次更新前端都会重新下载并替换发布包，即使版本号相同或显式指定了 `--frontend-version`，以获取同版本重新打包的内容
diff --git a/moviepilot b/moviepilot
index 900b36a03..23eebc211 100755
--- a/moviepilot
+++ b/moviepilot
@@ -202,6 +202,7 @@ Options:
 
 说明:
   - 更新后端依赖时会同步更新 moviepilot-rust PyPI 依赖
+  - 后端更新前如果检测到已跟踪源码改动，CLI 会询问是否清空本地改动；确认后才会继续更新，拒绝或非交互模式会取消更新
   - 可在前端“高级设置 - 实验室”中关闭或重新开启 Rust 加速
 EOF
 }
diff --git a/scripts/bootstrap-local.sh b/scripts/bootstrap-local.sh
index baaf56f25..896c812a4 100755
--- a/scripts/bootstrap-local.sh
+++ b/scripts/bootstrap-local.sh
@@ -69,9 +69,19 @@ sync_repo() {
 
   echo "==> 复用已有 MoviePilot 仓库: $APP_DIR"
   if repo_dirty "$APP_DIR"; then
-    echo "检测到现有仓库包含未提交改动，已停止自动更新。" >&2
-    echo "请先清理 $APP_DIR 的本地修改，或换一个新的安装目录后重试。" >&2
-    exit 1
+    echo "检测到现有仓库包含未提交的源码改动。"
+    if [[ "$NON_INTERACTIVE" != "true" && "$HAS_TTY" == "true" ]] && \
+      prompt_yes_no "是否清空本地改动并继续更新" "n"; then
+      (
+        cd "$APP_DIR"
+        git reset --hard HEAD
+      )
+      echo "==> 已清理本地已跟踪源码改动，继续更新"
+    else
+      echo "已取消更新，未清理 $APP_DIR 的本地改动。" >&2
+      echo "请先提交或清理本地修改，或换一个新的安装目录后重试。" >&2
+      exit 1
+    fi
   fi
 
   (
diff --git a/scripts/local_setup.py b/scripts/local_setup.py
index d7724c755..cbab2a263 100644
--- a/scripts/local_setup.py
+++ b/scripts/local_setup.py
@@ -3789,6 +3789,7 @@ def _git_output(*args: str) -> str:
 
 
 def _ensure_git_clean() -> None:
+    """检查源码工作树，并在用户确认后清除已跟踪的本地改动。"""
     status = _git_output("status", "--porcelain", "--untracked-files=no")
     if not status.strip():
         return
@@ -3806,9 +3807,18 @@ def _ensure_git_clean() -> None:
             preview += " 等"
         detail = f"：{preview}"
 
-    raise RuntimeError(
-        f"检测到当前仓库有未提交的源码改动{detail}，请先提交或清理后再执行更新。"
-    )
+    try:
+        confirmed = _prompt_yes_no(
+            f"检测到当前仓库有未提交的源码改动{detail}，是否清空本地改动并继续更新",
+            default=False,
+        )
+    except (EOFError, OSError) as exc:
+        raise RuntimeError("当前终端不支持交互确认，已取消更新。") from exc
+    if not confirmed:
+        raise RuntimeError("已取消更新，未清理本地源码改动。")
+
+    print_step("清理本地已跟踪源码改动")
+    run(["git", "reset", "--hard", "HEAD"], cwd=ROOT)
 
 
 def _update_backend_ref(ref: str, *, fetch: bool = True) -> str:
diff --git a/tests/test_local_setup_update.py b/tests/test_local_setup_update.py
new file mode 100644
index 000000000..4763be452
--- /dev/null
+++ b/tests/test_local_setup_update.py
@@ -0,0 +1,91 @@
+"""本地 CLI 更新遇到源码改动时的确认与清理测试。"""
+
+from __future__ import annotations
+
+import importlib.util
+import uuid
+from pathlib import Path
+
+import pytest
+
+
+MODULE_PATH = Path(__file__).resolve().parents[1] / "scripts" / "local_setup.py"
+
+
+def load_local_setup_module():
+    """加载独立的本地安装脚本模块，避免共享全局配置。"""
+    module_name = f"moviepilot_local_setup_update_{uuid.uuid4().hex}"
+    spec = importlib.util.spec_from_file_location(module_name, MODULE_PATH)
+    assert spec is not None and spec.loader is not None
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module
+
+
+def test_dirty_update_clears_tracked_changes_after_confirmation(monkeypatch):
+    """确认清理后应重置已跟踪源码改动，供后续 Git 更新继续。"""
+    module = load_local_setup_module()
+    prompts: list[tuple[str, bool]] = []
+    commands: list[list[str]] = []
+    monkeypatch.setattr(module, "_git_output", lambda *_args: " M app/example.py\n")
+    monkeypatch.setattr(
+        module,
+        "_prompt_yes_no",
+        lambda label, default: prompts.append((label, default)) or True,
+    )
+    monkeypatch.setattr(
+        module,
+        "run",
+        lambda command, cwd=None: commands.append(command),
+    )
+
+    module._ensure_git_clean()
+
+    assert prompts == [
+        (
+            "检测到当前仓库有未提交的源码改动：app/example.py，是否清空本地改动并继续更新",
+            False,
+        )
+    ]
+    assert commands == [["git", "reset", "--hard", "HEAD"]]
+
+
+def test_dirty_update_stops_when_local_change_cleanup_is_rejected(monkeypatch):
+    """拒绝清理时应取消更新且不执行任何 Git 写操作。"""
+    module = load_local_setup_module()
+    commands: list[list[str]] = []
+    monkeypatch.setattr(module, "_git_output", lambda *_args: " M app/example.py\n")
+    monkeypatch.setattr(module, "_prompt_yes_no", lambda *_args, **_kwargs: False)
+    monkeypatch.setattr(
+        module,
+        "run",
+        lambda command, cwd=None: commands.append(command),
+    )
+
+    with pytest.raises(RuntimeError, match="已取消更新"):
+        module._ensure_git_clean()
+
+    assert commands == []
+
+
+def test_dirty_update_stops_without_an_interactive_input(monkeypatch):
+    """没有可用输入时应取消更新，而不是默认清除源码改动。"""
+    module = load_local_setup_module()
+    commands: list[list[str]] = []
+    monkeypatch.setattr(module, "_git_output", lambda *_args: " M app/example.py\n")
+
+    def raise_eof(*_args, **_kwargs):
+        """模拟没有可用终端输入。"""
+        raise EOFError
+
+    monkeypatch.setattr(module, "_prompt_yes_no", raise_eof)
+    monkeypatch.setattr(
+        module,
+        "run",
+        lambda command, cwd=None: commands.append(command),
+    )
+
+    with pytest.raises(RuntimeError, match="不支持交互确认"):
+        module._ensure_git_clean()
+
+    assert commands == []