Abstract: Analyzing the spatio-temporal evolution process and mechanism of traditional villages can provide reference for village protection in the new era. Based on the genesis, focusing on the attribute of village “affairs”, combining with GIS technology, this paper analyzes the spatio-temporal evolution of 168 national and municipal traditional villages in Chongqing based on practice. The research reveals the following: (1) the practic is the root of village evolution, and has significant genetic effect on it. The historical fluctuation of practice drives the fluctuating development of villages: villages developed spontaneously in the pre-Qin period, fluctuated from the Qin and Han dynasties to the Song and Yuan dynasties, increased significantly in the Ming Dynasty, and laid a foundation for the pattern of contemporary villages from the Qing Dynasty to the Republic of China. (2) Agricultural, economic and political practices are the main practices that stimulate the evolution of villages. They promote the generation of agricultural, commercial and military villages respectively and have undergone transformation. Among them, the number of agricultural villages is the largest, and the transformation from agricultural to commercial villages is the most prominent. (3) Affected by the spatial evolution of practice, the villages are promoted from the main stream of the Yangtze River to the southeastern mountainous areas, and develop from scattered distribution to the whole region. Finally, a pattern of agricultural villages is formed in the eastern part of Chongqing, commercial ones in the west, and military ones in the main traffic routes is formed. (4) Guided by the practical purpose, it analyzes the genetic mechanism of the temporal and spatial evolution of villages, and then abstracts and constructs the logical structure of “practice environment -meta-practice”, and concludes that the evolution of villages is carried out in the unity of opposites between active and active. The results suggest that the protection of traditional villages requires a suitable practical environment and the maintenance of population and material production. We suggest to keep original practice, integrate creative practice, and promote ethical practice, so as to keep the vitality and reasonable development of the village in the continuation of the local.