Traditional villages (TVs) constitute an integral segment of China’s cultural heritage, encapsulating diverse values. This research scrutinizes 777 national-level TVs spanning six batches in Yunnan Province. Spatial distribution patterns were examined via the nearest neighbor index, kernel density, and Moran’s I. A comprehensive framework for driving factor analysis was devised, encompassing four principal categories and twelve subcategories of natural, spatial, social, and regional cultural factors. The driving factors influencing the distribution of TVs at the provincial scale were analyzed using geographically weighted regression (GWR) models and geodetector, thoroughly investigating the spatial autocorrelation and heterogeneity of TVs in Yunnan. The results reveal: (1) Three spatial nucleus areas of national-level TVs in Yunnan Province are discerned in western, northwestern, and southeastern Yunnan. The global Moran’s I is 0.66, with 61.9% of TVs displaying clustering. (2) The spatial configuration of national-level TVs in Yunnan Province is collectively impacted by twelve factors, exhibiting significant spatial heterogeneity. Natural factors dictate the location and development scale of TVs, with slopes exerting the strongest influence. Among spatial factors, the proximity between villages and roads manifests the most substantial impact. The driving force of per capita GDP, categorized as a social factor, attains a value of 0.119. Regional cultural factors present the strongest overall driving force, with intangible cultural heritage and cultural relic protection units generally demonstrating a positive correlation, albeit with some negative correlations in specific locales. (3) Intangible cultural heritage (X11) emerges as the single factor with the highest driving force, bearing a p-value of 0.326. The interaction between intangible cultural heritage (X11) and cultural relic protection units (X12) reveals the most robust interactive driving force, possessing an explanatory power of 0.745, indicating that these two factors, with the highest explanatory power, constitute the most critical driving combination. These insights can furnish decision-making support for the holistic development and preservation of TVs in plateau mountainous regions and guide the sustainable evolution of TV cultural heritage clusters in Yunnan.