The Yangtze River Basin (YRB) is the birthplace of Chinese civilization and is rich in traditional village resources. Studying their spatial distribution characteristics and influencing factors can guide the protection, inheritance, and development of traditional villages in YRB. This study takes 5 batches of 3346 traditional villages in YRB since 2012 as the research object. Using the nearest neighbor index, kernel density analysis, standard deviation ellipse, and Geodetector model, we analyzed the spatial distribution characteristics of traditional villages in YRB and detected their influencing factors. The results show that the distribution of traditional villages in YRB exhibited a spatial pattern of cohesive clusters, forming a high-density area and development center in the junction zone between Guizhou and Hunan provinces and southeast of Anhui Province, and secondary-density areas in Northeast Yunnan Province and east Jiangxi Province. The results of the Geodetector show that the formation of the spatial distribution pattern of traditional villages in YRB is affected by the combined effects of natural and socio-economic factors, among which elevation and NDVI were the main factors, and the interaction of multiple factors showed an enhanced trend. The findings of this study can provide scientific decision-making support for the development and protection of traditional villages in YRB.