Villages in rural areas are regional complexes with multiple characteristics and functions. Rural tourism has become an important driver in the revitalization of rural China. The Ministry of Culture and Tourism of China approved the first group of 320 National Key Villages for Rural Tourism (NKVRT) in 2019. This paper takes these first 320 NKVRT as the research object, using GIS as a tool to analyze and discuss their spatial distribution characteristics, and identifies how they are affected by certain influencing factors. The results show the following: (1) the spatial distribution of NKVRT in China exhibits obvious differences, generally characterized as dense in the southeast and sparse in the northwest. Moreover, the development of rural tourism is closely related to the level of urbanization and economic development in the surrounding areas. (2) The core density of NKVRT presents the spatial distribution characteristics as “independent and evident in the high-value areas, gradually decreasing outward in the remaining grade areas.” The spatial pattern of core density has a high degree of similarity with the agricultural strategic pattern of the main functional areas of the country. (3) The spatial distribution characteristics of NKVRT are associated with climate, population, topography, precipitation, elevation, land use, and economic development. The spatial distribution characteristics of different types of NKVRT are also distinct. These research results emphasize that the development and growth of rural tourism in China should not only consider the balance between regions, but also the influence of both natural factors and human factors.