【Objective】 National parks are one of the most important types of nature reserves in China. The reasonable functional zoning is conducive to better protect and utilize natural resources, to realize its multi-objective scientific management, and is important for protecting biodiversity and promoting ecological civilization significance. 【Methods】 In this study, the important protection level of the natural ecosystem in Potatso National Park was taken as the principal weight, and the effects of agriculture, community, transportation, population and other factors on the protection objectives of important ecosystems were weighted. The weight spatial overlap method was used for a spatial analysis, in which the functional zoning of the national park was divided, and its rationality was evaluated.【Results】 ① The spatial overlap method based on the weight of important ecological system protection goals was used to partition the national park in Shangri-La. While determining the importance of the ecological protection objectives, the impacts and demands of the park’s stakeholders were balanced to achieve the goal of both protection and development. ② According to the results of the zoning, Potatso National Park was divided into two main functional zones; the core protection area accounted for 53.35% and the general control area accounted for 46.65% of the total area. The important ecosystems in the core area accounted for a high proportion, high concentration, effective protection, and reasonable zoning results. ③ The Potatso’s functional zoning resulted in not only protection of the important sub-alpine dark coniferous forest ecosystem, but also in the enhancement of the scientific nature and functional zoning operability.【Conclusion】 The research results provide a theoretical basis for the construction, planning, protection and utilization of national parks, and a reference for the application of the functional zoning method of nature reserves.