Abstract: The integration and optimization of protected areas is an essential part of constructing the protected area system with national parks as the main body. It is a critical path to promote the establishment of a protected area system with scientific classification, rational distribution, strong protection and effective management. In order to solve the problems of overlapping, multiple management, unreasonable division and eco-fragmentation of protected areas, this research suggests an integrated optimization scheme of natural protected areas from the technical and operational perspectives. Based on the current situations of resources and protection status, the scheme is obtained through value assessment of resources and exploration of the five tasks of integration, combination, optimization, transformation and gap filling. This research will provide a reference for the integration and optimization in protected areas in China.