Abstract: A relatively mature system of nature protected areas has been formed in Yangtze Basin. Revealing spatial distribution characteristics of nature protected areas and influencing factors can provide a scientific basis for the declaration, management, protection and sustainable development of nature protected areas in the watershed. Taking five types of national nature protected areas with a large number of Yangtze Basin as the research object, the spatial distribution differences of their quantity, area, geographic concentration and kernel density were analyzed, and the impact factors were discussed in depth. The results showed that: (1) There are a large number of national nature protected areas in Hunan, Sichuan, Jiangxi, Hubei, and Guizhou, with 152, 141, 125, 98, and 73 respectively. The total area of national nature protected areas of Qinghai, Sichuan, Hunan, Hubei, and Jiangxi has advantages, reaching 19 741 617, 3 893 913, 924 177, 739 134, and 643 504 km2 respectively. (2) National nature reserves (7.10), national scenic spots (7.16), and national water conservancy scenic areas (7.84) have the highest geographic concentration index in Hunan. National forest parks and national geological parks have the highest geographic concentration index in Jiangxi (7.24) and Guizhou (4.01) respectively. (3) The bandwidth value of the kernel density analysis for national nature reserves, national scenic spots, national forest parks, national water conservancy scenic spots, and national geological parks determined by the Ripley’s K method in Yangtze Basin are 20, 20, 20, 20, 25 km respectively. The spatial distribution of national nature reserves presents a pattern of one horizontal and two vertical strips. The spatial distribution of national scenic spots presents a pattern of one cluster in the lower reaches, two groups in the middle reaches, and a single hot core in the upper reaches. The spatial distribution of national forest parks presents a pattern of one cluster in the lower reaches, three clusters in the middle reaches, and a single core in the upper reaches. The spatial distribution of national water conservancy scenic spots presents a pattern of a single core in the lower reaches, two clusters in the middle reaches, and two cores in the upper reaches. The spatial distribution of national geological parks presents a pattern of one cluster in the lower reaches and one horizontal and two vertical strips in the middle and upper reaches. (4) The spatial distribution of various types of national nature protected areas is comprehensively affected by many different factors such as topography, vegetation, water resources, biodiversity, population, land, capital, transportation, and policy.