The establishment of a national park system is a key reform task proposed by the Third Plenary Session of the 18th Central Committee of the Communist Party of China. To achieve the target of ecological protection, functional zoning and space management are important to planning of national parks. Selecting the Three-River-Source National Park (TNP) as the study area, this paper explains the measures of functional zoning and space management, and analyzes the effect of ecological protection from the perspective of ecological restoration and biodiversity based on the actual monitoring data of the ecosystem, hoping to provide new insights into national parks' functional zoning and management measures.