In view of the problems of disordered land use structure before and after water storage in the Three Gorges Reservoir area and the contradiction between urban development and ecological protection, this paper proposes to guide the rational use of land effectively and promote the sustainable development of regional land resources through the health evaluation of land use system. Based on the analysis of the health connotation of the land use system, a triangular model based evaluation index system is constructed to make an empirical analysis of the Chongqing section of the reservoir area. The results showed that from 2000 to 2017, the health status of the land use system in the Three Gorges Reservoir area (Chongqing section)was continuously improved, and the whole land use system experienced the evolution process of "unhealthy, subhealthy and primary health",the overall spatial characteristics of health state showed that western Chongqing and southeast Chongqing were better than northeast Chongqing,the change trend of health status is generally good, mainly in primary health (T1, T3). The research results can reflect the development trend of the healthy state of the land use system in the region and realize the benign operation of the land use system.