Traditionally, “ancient villages” are communities that date back to a previous era, possess abundant traditional resources, and hold significant historical, social, cultural, ecological, and economic significance. This study examines the geographical and chronological development of 2957 traditional communities in the Yangtze River Basin and extensively employs GIS spatial analysis, geostatistical analysis, and historical literature review to study the evolution of the locations of traditional settlements under various factors. The study’s findings revealed that: (1) From a geographical standpoint, the traditional villages in the study area present a distribution state of “two cores, small aggregation, and many dispersions”. The two core clusters are located at the intersection of Hunan, Guizhou, and Chongqing provinces, where the natural geographical advantages attracted people from different dynasties to settle here. (2) From a temporal perspective, the quantity of traditional villages shows a growing trend, and the distribution center of each dynasty shows an east–west direction. Among them, the shift from the Song to the Yuan dynasties marked the period of greatest change in village distribution, which originated from the Song Dynasty’s quick economic growth. In addition, the village distribution was clustered in the eastern part of the country, adapting to the needs of commercial trade. When the Song Dynasty fell, the society was in turmoil, and the villages were transferred to the central region to avoid the war. The Yuan Dynasty also laid down the fundamental distribution pattern of conventional villages. (3) From the standpoint of choosing a village location, most of them are distributed in mountainous, hilly, and plain regions; the gentle slopes of 0°~15° are favored by people. Sufficient water sources, abundant precipitation, and a suitable climate are also necessary choices. (4) From the perspective of driving factors, traditional village distribution in the basin is impacted by historical, cultural, social, and ecological factors. Included among these, traditional village distribution is inversely connected with socio-economic variables. Under the interaction of two factors, the distribution will be more affected. To summarize, the complex human geographic factors together create the conventional village dispersal pattern, and examining these elements holds substantial practical importance for comprehending, safeguarding, and preserving traditional villages.