Traditional villages are important carriers of traditional cultural heritage, and they have strong historical, cultural, aesthetic and tourism value for all countries and the international community. In China, the number of traditional villages is currently decreasing each year, and the precious material and non-material heritage is at risk of disappearing in the process of urbanization. A comprehensive understanding of the spatiotemporal patterns of traditional villages on multiple scales has important significance in protecting traditional culture, revitalizing traditional villages and achieving sustainable urbanization. Therefore, the spatiotemporal characteristics of traditional villages at the city, province, and geographic zone scales are explored by a series of Geographic Information System(GIS)-based methods in this article. Specifically, the analysis units are multi-scale, the applied methods are multi-variate, and the identified patterns are multi-perspective. The results demonstrate that the distribution of traditional villages in China is unbalanced over space and time. Moreover, the different spatiotemporal distributions of traditional villages are sensitive to scales. These findings clarify differences in the corresponding geographic and environmental factors, the level of economic development and local policy support. We further suggest that exploring the effective and suitable modes of protection and rural development is necessary. The results of this article revealing the unbalanced spatiotemporal distribution of traditional villages can provide valuable suggestions and insights into alleviating regional inequality in China.