The study of the overall spatial distribution of traditional villages is of great significance for a comprehensive understanding of traditional villages from the perspectives of nature, economy, society, and culture. Taking the top six batches of national level traditional villages in Southeastern Shanxi as the research object, this study quantitatively investigates the factors affecting the spatial distribution of traditional villages using methods such as nearest neighbor index, Moran index, and quantitative geography. The study explores the factors such as terrain, watershed, and transportation that affect the spatial distribution of traditional villages. The results show that: 1) the overall distribution of traditional villages in Southeastern Shanxi presents a clustered geographical spatial feature, with a distribution pattern of “dual cores and one belt”. 2) The spatial distribution of traditional villages is the result of the combined effects of terrain, water systems, economic development level, transportation network, and other factors. The natural environment is the basic factor affecting distribution, while cultural economy is the internal driving force for village development. Based on the above results analysis, it is necessary to actively explore a cluster based protection framework for the current situation of traditional village protection in Southeastern Shanxi. According to the different degrees of impact of each element on traditional villages, the connection and role between each element should be strengthened as a reference for formulating differentiated policies.