To promote the construction of an ecological civilization and an eco-friendly China, a rational use of natural resources, and harmony between human beings and nature, China has proposed a "national park system", seeking for the optimization and improvement of the complete protected areas system. Functional zoning, the most relevant process in protected area planning and management, is an integral part of the optimization of the system. Natural parks, an important part of these protected areas, also have many problems with functional zoning; for example, the inadequate coordination between the development of both the ecology and economy and the lack of studies for a comprehensive planning have not led to a sustainable development of these protected areas. Therefore, to solve these zoning issues, this study proposes a comprehensive functional zoning method for natural parks, applying it to the Huangshan Scenic Area as an example. The method is based on the assessment of irreplaceability, ecological vulnerability, condition of landscape resources, and ecological suitability. From a functional perspective, natural parks can be first divided into protected ecological, protected landscape, and developmental zones. Both the protected ecological and landscape zones can be further subdivided into core and important zones. In addition, the developmental zone can be further subdivided into recreational, agricultural, and living zones.