Ancient towns in water towns are traditional settlement landscapes with unique landscape characteristics, carrying and inheriting native culture. Landscape gene recognition theory has a systematic and scientific way of analysis and assessment in the research of traditional settlement landscape features and historical and cultural characteristics, which is conducive to the effective protection and development of traditional settlement landscapes. This paper takes Jiaoxi Ancient Town as an example, introduces the theory of landscape gene recognition, summarises and evaluates its recessive and dominant landscape genes, constructs a landscape gene map of Jiaoxi, excavates the landscape gene structure features from the environmental and village scales, and summarises the landscape features from the three perspectives of landscape pattern, ecological wisdom and layout construction. The results show that: (1) On the environmental scale, Jiaoxi water town has the environmental pattern of three mountains and two waters, and at the same time, it retains the spatial structure of a relatively complete trade town, which is of high conservation value. (2) On the village scale, the distribution of Jiaoxi landscape gene points concentrates on the formation of two core corridors, constituting the unique structure of bridge - river - street - lane - circle - gate, but some of the landscape components exist in the status quo of being damaged and non-existing. Jiaoxi has a rich variety of landscape genes, which are related to ecology, production, and life. They form the natural pattern of mountain - river - field - village, some of which are also developed continuously as local agricultural by-products. The improvement and construction of the future research system of ancient water towns still need continuous extensive cooperation and in-depth related research to provide new ideas for the protection and development of ancient water towns.