This paper aims to analyze the distribution patterns of the Yunnan, Guangxi, and Guizhou rocky desertification area, and provide efficient protection and development strategies. This region has a complex geographical environment, and it is distinguished by hosting China’s largest ethnic minority population and the highest concentration of autonomous ethnic counties among contiguous impoverished areas, with numerous traditional villages. Thus, it is significant to conduct a comprehensive study of traditional villages within this domain, with a particular focus on their centralized preservation and strategic utilization. This research employed ArcGIS and Geodetector software for a rigorous analysis of the spatial distribution characteristics and influential factors of traditional villages in the Yunnan, Guangxi, and Guizhou rocky desertification area. The key findings can be summarized as follows. (1) The traditional villages in this region predominantly exhibit an agglomerative distribution pattern, with pronounced concentrations in southeast Guizhou and secondary concentrations in Anshun and Guilin. (2) Natural environmental factors, social economic factors, and national cultural factors impact the distribution of traditional villages synthetically by positive, median, or negative correlation. (3) The results of the Geodetector show that, significantly, social economic and national cultural factors exert a more pronounced influence than natural environmental factors, especially population density and intangible heritage quantity. The interaction of multiple factors shows an enhanced trend. (4) From the perspective of formation mechanism, natural environmental factors serve as foundational elements shaping the original distribution pattern; national cultural factors act as dominant determinants, accentuating spatial distribution distinctions across various regions and social economic factors emerge as critical catalysts for the sustainable development of traditional villages. The interaction factors can have a more profound impact. Furthermore, it is expected that this study will contribute to the effectiveness of ecology and economy in this area and more analogous regions.