Abstract: Spatial gene theory is an important framework system to solve the problems of spatial development and cultural inheritance in characteristic villages and towns. However, current research focuses on the identification, extraction, inheritance, and application of spatial genes, and there is a lack of research on how to integrate spatial genes into the existing spatial planning system. This paper sorted out the protection and inheritance system under the territorial spatial planning system. And on the basis of existing research, it proposed that the identification and extraction of spatial genes was the premise, the feasibility analysis of spatial gene inheritance was the key, and the construction of spatial gene protection and inheritance planning system was the core research idea. Finally, taking Jiuxian Village of Guilin City, Guangxi Zhuang Autonomous Region as a study case, the spatial gene identification and extraction of Jiuxian Village were carried out according to the above points, and the spatial gene protection and inheritance planning of Jiuxian Village was studied in combination with the relevant planning of Jiuxian Village.