Landscape Gene Theory has opened up a new research perspective for the protection and development of traditional villages, with water landscapes playing an irreplaceable role in their formation and evolution. To emphasize the importance of extracting and expressing the genes of traditional village water landscapes in preserving and continuing traditional villages, this study focuses on the water landscape genes of traditional villages. Taking the typical traditional village of Hongcun as an example, it adopts N-level Coding Theory and follows the coding rule of "object - character - text - N-level recreation". Based on cultural classification standards, the traditional village waterfall landscape genes are categorized, and their relational sequence structure is constructed to clarify the expression mechanism between external performance traits and internal cultural connotations of these water landscape genes. Research has shown that the traditional village water landscape genes that return to culture include two main categories: material water landscape genes and cultural water landscape genes, along with nine subcategories including village site selection and overall layout. The relationship sequence structure of traditional village water landscape genes manifests as six specific paths of "material-culture", specifically, "external trait expression-internal cultural manifestation". This research enhances the theory of traditional village landscape genes, supplements the research perspective on landscape genes, and has clear guiding implications for the renovation of traditional village water landscapes and the protection and continuity of traditional culture in practice.