The landscape genes are born from the genetic concept of biology and can play an active role in the internal mechanism and external expression of the spatial characteristics of traditional settlements. The landscape genes are the key elements to distinguish the characteristics of each type, and the emphasis on the causes of the evolution of material forms and spatial and temporal conditions can, to a certain extent, effectively help to study the regular characteristics of the traditional village landscape. Based on landscape genes, this paper studies the spatial characteristics of traditional villages and their inheritance and protection mechanisms, to construct a traditional village landscape genetic system and verify its scientificity by taking Huizhou traditional villages as an example. In order to provide some reference for the study of spatial characteristics of traditional villages and the inheritance and protection of traditional villages.