diff --git a/src/core/config.ts b/src/core/config.ts
new file mode 100644
index 0000000..57c4e82
--- /dev/null
+++ b/src/core/config.ts
@@ -0,0 +1,66 @@
+import { existsSync } from "node:fs";
+import { readFile } from "node:fs/promises";
+import { join, dirname } from "node:path";
+import { parse as parseYaml } from "yaml";
+import { defaultConfig } from "../defaults/config.ts";
+import type { RuneConfig } from "../types.ts";
+import { RUNE_DIR, CONFIG_FILE, CHANGES_DIR, ARCHIVE_DIR } from "../types.ts";
+
+export function findProjectRoot(
+  startDir: string = process.cwd(),
+): string | null {
+  let dir = startDir;
+  while (true) {
+    if (existsSync(join(dir, RUNE_DIR))) {
+      return dir;
+    }
+    const parent = dirname(dir);
+    if (parent === dir) return null;
+    dir = parent;
+  }
+}
+
+export async function loadConfig(projectRoot: string): Promise<RuneConfig> {
+  const configPath = join(projectRoot, RUNE_DIR, CONFIG_FILE);
+  try {
+    const content = await readFile(configPath, "utf-8");
+    const userConfig = parseYaml(content) as Partial<RuneConfig> | null;
+    if (!userConfig?.stages) {
+      return structuredClone(defaultConfig);
+    }
+    return mergeConfig(userConfig);
+  } catch {
+    return structuredClone(defaultConfig);
+  }
+}
+
+function mergeConfig(userConfig: Partial<RuneConfig>): RuneConfig {
+  const result: RuneConfig = { stages: {} };
+  const stageKeys = ["discuss", "plan", "build", "archive"] as const;
+
+  for (const stage of stageKeys) {
+    if (userConfig.stages?.[stage]) {
+      result.stages[stage] = userConfig.stages[stage]!;
+    } else if (defaultConfig.stages[stage]) {
+      result.stages[stage] = structuredClone(defaultConfig.stages[stage]!);
+    }
+  }
+
+  return result;
+}
+
+export function getRuneDir(projectRoot: string): string {
+  return join(projectRoot, RUNE_DIR);
+}
+
+export function getChangesDir(projectRoot: string): string {
+  return join(projectRoot, RUNE_DIR, CHANGES_DIR);
+}
+
+export function getArchiveDir(projectRoot: string): string {
+  return join(projectRoot, RUNE_DIR, ARCHIVE_DIR);
+}
+
+export function getChangeDir(projectRoot: string, changeName: string): string {
+  return join(projectRoot, RUNE_DIR, CHANGES_DIR, changeName);
+}
diff --git a/tests/core/config.test.ts b/tests/core/config.test.ts
new file mode 100644
index 0000000..b68a1b0
--- /dev/null
+++ b/tests/core/config.test.ts
@@ -0,0 +1,94 @@
+import { describe, it, expect, beforeEach, afterEach } from "bun:test";
+import { mkdir, writeFile, rm } from "node:fs/promises";
+import { join } from "node:path";
+import { loadConfig, findProjectRoot, getRuneDir } from "../../src/core/config.ts";
+
+const TMP_DIR = join(import.meta.dir, "__tmp_config_test__");
+
+beforeEach(async () => {
+  await mkdir(TMP_DIR, { recursive: true });
+});
+
+afterEach(async () => {
+  await rm(TMP_DIR, { recursive: true, force: true });
+});
+
+describe("findProjectRoot", () => {
+  it("当前目录存在 .rune/ 时返回当前目录", async () => {
+    await mkdir(join(TMP_DIR, ".rune"));
+    expect(findProjectRoot(TMP_DIR)).toBe(TMP_DIR);
+  });
+
+  it("子目录中向上查找到 .rune/", async () => {
+    await mkdir(join(TMP_DIR, ".rune"));
+    const sub = join(TMP_DIR, "src", "commands");
+    await mkdir(sub, { recursive: true });
+    expect(findProjectRoot(sub)).toBe(TMP_DIR);
+  });
+
+  it("找不到 .rune/ 时返回 null", () => {
+    expect(findProjectRoot("/tmp/__nonexistent__")).toBeNull();
+  });
+});
+
+describe("loadConfig", () => {
+  it("无配置文件时返回默认配置", async () => {
+    await mkdir(join(TMP_DIR, ".rune"));
+    const config = await loadConfig(TMP_DIR);
+    expect(config.stages.discuss).toBeDefined();
+    expect(config.stages.plan).toBeDefined();
+    expect(config.stages.build).toBeDefined();
+    expect(config.stages.archive).toBeDefined();
+  });
+
+  it("用户配置覆盖默认配置（全量替换）", async () => {
+    const runeDir = join(TMP_DIR, ".rune");
+    await mkdir(runeDir, { recursive: true });
+    await writeFile(
+      join(runeDir, "config.yaml"),
+      `stages:
+  discuss:
+    prompt: 自定义讨论提示词
+`,
+    );
+    const config = await loadConfig(TMP_DIR);
+    expect(config.stages.discuss!.prompt).toBe("自定义讨论提示词");
+    expect(config.stages.plan).toBeDefined();
+    expect(config.stages.build).toBeDefined();
+    expect(config.stages.archive).toBeDefined();
+  });
+
+  it("用户配置 plan 时完全替换内置 documents", async () => {
+    const runeDir = join(TMP_DIR, ".rune");
+    await mkdir(runeDir, { recursive: true });
+    await writeFile(
+      join(runeDir, "config.yaml"),
+      `stages:
+  plan:
+    documents:
+      - name: spec
+        prompt: 生成规格文档
+`,
+    );
+    const config = await loadConfig(TMP_DIR);
+    expect(config.stages.plan!.documents).toHaveLength(1);
+    expect(config.stages.plan!.documents[0].name).toBe("spec");
+  });
+
+  it("YAML 解析错误时返回默认配置", async () => {
+    const runeDir = join(TMP_DIR, ".rune");
+    await mkdir(runeDir, { recursive: true });
+    await writeFile(
+      join(runeDir, "config.yaml"),
+      `stages: [invalid yaml {{{`,
+    );
+    const config = await loadConfig(TMP_DIR);
+    expect(config.stages.discuss).toBeDefined();
+  });
+});
+
+describe("getRuneDir", () => {
+  it("返回 .rune 目录路径", () => {
+    expect(getRuneDir("/project")).toBe("/project/.rune");
+  });
+});