The Yuan River Basin in Hunan Province, known for its rich history and cultural heritage, is home to traditional village landscapes characterized by distinct cultural genes and regional features. This study focuses on 21 traditional villages in Xupu County, Huaihua, and develops four types of traditional village landscape cultural genome atlases at three hierarchical levels: individual villages, multiple villages, and a specific research area. These atlases include genetic linkage maps, spatial sequence maps, distribution pattern maps, and geographical pattern maps. Using Yangquepo in Zhumucun Village as a case study, we constructed a genetic linkage map for the landscape cultural genome of a single traditional village, based on the arrangement structure of courtyard layouts. Spatial sequence maps were derived from the overall spatial configuration, while distribution pattern maps and geographical pattern maps for the 21 villages were developed using kernel density analysis in ArcGIS 10.8 software. The results reveal that traditional village landscapes in the region possess a diverse cultural genome, marked by distinct regional characteristics and spatial organization patterns.