Traditional villages (TVs) are clusters for the conservation of farming civilization heritage with multiple values. Studying their spatial distribution and driving mechanisms is conducive to formulating conservation and development strategies. In this study, 777 TVs in Yunnan Province were examined. Spatial analysis methods such as the nearest neighbor index (NNI), kernel density estimation (KDE), and Moran’s I were used to investigate their spatial distribution patterns. Twelve driving factors were selected from natural, spatial, social, and cultural aspects. The driving mechanisms affecting the distribution of TVs were explored by employing the geographically weighted regression (GWR) model and Geodetector combined with mathematical and statistical methods to systematically study the spatial autocorrelation and heterogeneity of TVs in Yunnan. The results of this study indicate that: (1) The 777 TVs in Yunnan Province are evidently clustered in the overall distribution, presenting a contiguous and concentrated distribution pattern of “3 high-density areas + multiple medium-density belts”. However, the distribution of TVs is unbalanced. The spatial distribution is significantly positively correlated globally, and there exist three types of clustering in local areas. (2) The spatial layout of TVs in Yunnan Province is jointly influenced by multiple factors, with obvious spatial heterogeneity. Regional cultural factors are the key ones. TVs tend to be distributed in areas with medium–high elevation, flat slops, sunny slopes, moderate precipitation and temperatures, and a certain distance from water sources and roads. A large number of TVs are distributed in areas with a high proportion of ethnic minorities. (3) The main factors affecting the distribution of national-level TVs in Yunnan are intangible cultural heritage, cultural relic protection units, followed by factors such as transportation, slope, and elevation. The interaction between intangible cultural heritage (X11) and cultural relic protection units (X12) reveals the strongest interactive driving force. This study reveals the diverse characteristics of the spatial distribution of national-level TVs in Yunnan and their influencing mechanisms, which can provide a scientific decision-making basis for the future protection and development of TVs in Yunnan and guide the sustainable development of TV cultural heritage clusters.