Traditional villages are the place where national culture is nurtured and inherited. Due to the acceleration of urbanization, the protective exploitation of traditional villages is an urgency in many regions of the world. Under the perspective of the “Space Gene”, we define the connotation of the traditional village space gene, which refers not only to a space combination model, but also the basic inheritance unit of the sustainable development of traditional villages. We further propose the Quantitative Inheritance System Model of Traditional Village Space Genes, which reveals the logic behind the formation of traditional village material forms and builds a quantitative index system for traditional village forms. We take Shibadong Village as an example to prove the model. The results demonstrate that although the four camps in Shibadong Village belong to the same ethnic group and the same village, there are still apparent differences in morphological features. Through the model, we can turn from the “built form” research from the perspective of material space to the “deep structure” research behind it, which can provide scientific guidance for the planning and designs of traditional villages to inherit the history and culture and to protect the diversity of world culture.

In the context of global urbanization, traditional villages have garnered increasing scholarly interest due to their role in preserving rich ethnic cultures and their potential contributions to cultural heritage. Existing literature has predominantly attributed the spatial heterogeneity of traditional villages to natural, environmental, and economic factors. However, cultural elements, which are equally crucial to the inheritance and continuation of traditional villages, are rather deficient in current research. By establishing a tripartite framework encompassing “natural environment—space economy—social culture” elements, this article first employs relevant geographic spatial analysis to examine the overall distribution patterns of Chinese traditional villages. Subsequently, it utilizes the Optimal Parameter-based GeoDetector model to assess the maximum impact of single factors and interactions among factors on the spatial heterogeneity of Chinese traditional villages. The paper then integrates spatial production theory to reveal the mechanisms underlying the interactions among these tripartite elements. The research findings indicate that cultural factors exert the most substantial influence on the spatial distribution of traditional Chinese villages, in contrast to previous research records that suggested natural elements had the greatest impact. Additionally, population and genealogy emerge as the two most critical factors, with their interaction having the most significant effect on the spatial pattern of Chinese traditional villages (q = 0.82663). Finally, we put forward regional-level recommendations for the preservation of traditional villages. Overall, our work can not only provide valuable insights for global research on traditional villages in developing countries based on traditional agriculture but also offer recommendations for the preservation of traditional villages in China.