There are various types of natural protected areas in China, and the level of protected area is systematic. But due to multi-management and unclear authority, the borders of natural protected areas were confused and overlapped seriously. Making the spatial distribution and overlapping of natural protected areas clear in China is an important basis for constructing the system of natural protected areas dominated by national parks, which can provide an effective basis for the scientific optimization and integration of new natural protected areas in China. The Yangtze river economic belt plays an important role in ecological protection, being as an important area of ecology, life and production in China, the previous problems are still obvious. In our study, a total of 2383 vector boundaries of 6 types of natural protected areas in 11 provinces of the Yangtze River economic belt were collected. Based on the overlapping relationship model, the boundary overlapping relationships between different types of natural protected areas are analyzed, and the systematic suggestions are further given. The results are as following: (1) The number of overlapping relationships among natural protected areas is 1296, which accounts for 54.4% of the total number of boundaries of acquired protected land. The overlapping area is 29728.4 square kilometers, accounting for 11.4% of the total area of the acquired natural protected area. In general, there have large of overlapping areas in the west and the middle part of China, yet small overlapping area in the east of China as well. (2) In terms of the groups of relative overlap areas, there are 1138 groups of natural protected areas with one overlap, 249 groups with two overlaps, 17 groups with three overlaps, and no four or more overlaps. (3) In terms of the numbers of absolute overlap areas, there are numbers of 56 natural protected areas which overlap with other 5 or more natural protected areas synchronously, and the Dabie Mountain National Geopark with the largest number of overlaps with other 15 natural protected areas. (4) On the base of analysis and policy research of the overlapping areas, we put forward the integration strategies for different characteristics of overlapping areas, including boundary adjustment, consolidation and type integration, and extracts overlapping hot spots, which expect to provide data support for the integration of natural reserves and the construction of national parks, and also provide a reference scheme to the urgent needs of ongoing reform of China's natural protected areas system.