Rural tourism resources are the core carriers of rural tourism. It is, therefore, beneficial to further optimize the layout of rural tourism and to explore the spatial differentiation of rural tourism resources and their influencing factors. Taking 4670 rural tourism resources in Guangdong Province in China as the research object, this study explores the spatial distribution patterns of rural tourism resources through the nearest neighbor index, grid dimension analysis, kernel density analysis, and standard deviation ellipse method. Geodetectors are used to identify the influencing factors of the spatial heterogeneity of these resources in Guangdong Province. The findings reveal the following: (1) The distribution of rural tourism resources in Guangdong Province shows a tendency of agglomeration along the Tropic of Cancer, and the spatial distribution is unbalanced. The hot and cold spots show a “northeast-southwest” distribution trend. Furthermore, most of the hotspots form three high-density core areas, the sub-dense stretch zones connect into a w-shaped belt, and the sub-cold areas and sub-hot areas show a large expansion trend, thus forming five radiation areas. (2) The distribution of rural tourism resources in Guangdong Province is affected by multiple factors. In particular, the force of agricultural resource endowment, tourism resource endowment and transportation location are relatively strong, and social economy and tourist source market are the weak factors.