Rural settlements serve as spatial carriers of the micro-scale human-environment regional system. Within the parallel ridge-valley and mesa-hilly regions of Chongqing, there exists a distinct type of rural settlement that has long been overlooked. Based on toponymic semantic tracing, GIS spatial analysis, and locality theory, this study systematically elaborates the conceptual connotation of “Wanluo settlements”, quantifies their spatial differentiation characteristics, and identifies their core landscape genes. The research findings are summarized as follows: 1) Chongqing Wanluo settlements represent unique settlement units constructed by ancient Bayu inhabitants in adapting to micro-topographies in hilly and mountainous terrain. They exhibit prominent spatial agglomeration and follow a core-periphery concentric circle structure. 2) Site selection of Chongqing Wanluo settlements adheres to the logic of “micro catchment habitats”. Micro-geomorphic factors including elevation, slope gradient, and slope aspect demonstrate substantially higher explanatory power than distance to water systems. 3) This study identifies three-dimensional landscape genes spanning environment, structure, and culture, alongside a symbiotic system integrating production, habitation, and community. Four typical morphological categories of wan settlements are further classified: isolated, elongated, bifurcated, and clustered types. This research verifies the intrinsic independent value of Chongqing Wanluo settlements as an ecologically resilient human settlement paradigm. It provides a scientific foundation for differentiated conservation of traditional Bayu landscapes and the construction of distinctive living environments in the context of rural revitalization strategy.