Abstract: The number of rural settlements in China is large, and the regional differences are obvious. Indepth study of the morphological characteristics and development and evolution of regional rural settlements is urgent to explore the inheritance of regional characteristics. Analogizing the concept of biological gene, the article defines the spatial genes of rural settlements as factors that control the characteristics of the settlements, including space organizational rules (space genes) and their key influencing factors (morphogenic genes). This paper establishes a spatial characteristics analysis framework, and takes Chongqing's historical and cultural villages and industrial characteristic villages as examples to analyze the characteristics and evolution of the land form and composition of rural settlements, building composition and texture, and reveals the relatively stable spatial model. It also analyzes its influencing factors and the evolution mechanism in the geographical environment, social and economic aspects. Finally, it reveals the space gene and their different forms in various conditions, constructs a spatial gene map combining influencing factors and spatial forms, and explores the enlightenment for rural planning and design.