The construction of natural protected area system is a biodiversity conservation strategy which has been highly emphasized by international communities. In recent years, China expresses its concerns about the overlapping and intersection of natural protected area and proposed Guidance on Establishing a Natural Protected Area System Dominated by National Parks. To implement the proposed strategy, it is important to conduct a systematic study on the relationship and spatial distribution of the natural protected areas. This study collected data from 8,572 natural protected areas in different categories and administrative levels, including coordinates, types of ecosystems, administrative regions and boundaries. Among them, 1,532 natural protected areas with spatial overlapping and cross-jurisdictions were selected. Geographic concentration index (G) was calculated, and ArcGIS software was adopted for Kernel density estimation. Finally, the spatial distribution patterns, overlap of protected areas in ecological and geographic zones, ecosystem types, agencies with crossing jurisdiction and province locations were obtained. The results showed that: (1) Natural protected areas were concentrated in mountainous areas in central Shandong, Taihang Mountain, Dabie Mountain, Tianmu-Huaiyu Mountain and Wanjiang region, across multiple wetlands and forest ecosystems (Mean > 6, Max > 8). Among 10 pilot national parks, only Giant panda, Nanshan and Qianjiangyuan were located in areas with high density of overlapping; (2) The former State Administration of Forestry and the Ministry of Housing and Urban-rural Development had the largest number of sites under cross-jurisdiction among all the former agencies; (3) The number of overlapping natural protected areas in Heilongjiang, Anhui, Shandong, Henan, Hubei and Hunan provinces are significantly higher than other provinces. The overlap between Shanxi-Hebei-Henan and Anhui-Hubei-Jiangxi provinces is higher, and there is moderate overlap in other provinces. The areas studied above could become key priority areas for reassembling and optimizing China’s protected area system. Based on overlap hot zones, priority zones for biodiversity conservation, and cultural ecosystem services, this paper proposes a framework for reassembling and optimizing overlapped protected areas. According to 3 new protected area categories including national parks, nature reserves and natural parks, suggestions are given prioritizing reassembling and associating the area with a new category, which would provide a reference scheme to the urgent needs of ongoing reform of China’s natural protected areas system.