Abstract: As China is in the stage of reforming the protected area system, addressing the juxtaposition and overlapping management of protected areas has become a priority and research focus of the optimization and integration of protected areas. Clarifying the overlapping characteristics of various types of protected areas is a key step in the optimization and integration, which provides a baseline reference for adjusting the boundaries of protected areas. This research takes Fujian, a province known for overlapping protected areas, as the target, and analyzes the spatial relations of the local overlapping protected areas on the basis of ArcGIS, as well as the distribution characteristics of the overlapping space of the protected areas in terms of physical geography and social economy. The results show that: 1) The overlapping of protected areas in Fujian comprises three spatial types, which are the complete overlapping, partial overlapping, and embedded overlapping. Among them, partial overlapping is the most representative. 2) In terms of physical geography, the spatial overlapping of protected areas in Fujian Province mainly takes place in ecotones and economically underdeveloped areas of rich water resources, high vegetation coverage. 3) In terms of social economy, the spatial overlapping areas is mainly located in the economically underdeveloped areas, and places close to the road and urban and rural construction land. This research, on the basis of analyzing the distribution characteristics and key influencing factors of the overlapping landscape, puts forward measures to optimize the spatial integration and management mechanism for various types of spatial overlapping, and provides technical support and policy advice for the optimization and integration of protected areas in the province and reference for the reform of China’s protected area system.