【Objective】The aim of this study is to conduct a quantitative analysis of the overlapping characteristics of national natural protected areas in the middle Yangtze River basin and their optimization and integration strategies. This could provide a scientific basis for rational planning and layout of natural protected areas in China. 【Method】The 661 national natural protected areas in the middle Yangtze River basin were classified into six types and used as the research object. This study quantitatively revealed their overlapping characteristics and optimized integration strategies by using the ArcGIS nearest neighbor index and nuclear density index. 【Result】We found 214 overlapping national natural protected areas in the middle Yangtze River basin, mainly concentrated in the Poyang Lake, South of the Dabie Mountains Wuling Mountains and Funiu Mountains, as well as provincial administrative divisions, river basin divisions, biodiversity conservation priority areas, and ecological function protection areas. Priority should be given to the above areas for optimization and integration and type integration. Moreover, similar mergers, absorption mergers, and scope adjustments should be carried out with national parks, nature reserves, scenic spots, and natural parks as goals. 【Conclusion】Using the ArcGIS quantitative visualization overlay analysis method, the problem of overlapping of natural protected areas can be effectively solved, which is conducive to the scientific construction of a country’s nature reserve system and its spatial pattern planning.