Reasonable natural resource protection zones of national park could help to conserve the natural resource pertinently and enhance the protective effect. Taking the Beijing Great Wall National Park System Pilot Area as an example, this paper selects the indicators from the three aspects of "ecological background", "resource characteristics" and "human interference" to construct an index system for natural resources protection zoning. Using subcompartment as a zoning unit, the national park is divided into seven natural resource protection areas at first according to the ecological background characteristics, which are used as the basic units for resource survey and management of national parks. Then the national park are further subdivided into 17 kinds of natural resource protection areas according to the specific resource problems and protection demands, forming a two-level natural resource protection zoning scheme. Furthermore, corresponding protection measures are proposed based on the protection objectives of each protected area. The zoning scheme avoids the difficulty of coordination caused by the overlapping or misplaced space layout of various types of land in the national park. Moreover, it is also conducive to the implementation of natural resource protection zoning scheme and the effective protection of natural resources in the national park.