The Three Gorges reservoir area forms an ecological barrier for the key sensitive areas of the middle and lower reaches of the Yangtze River. The ecological quality of a land use system is directly related to the overall benefits of the Three Gorges Project and to the ecological security of the middle and lower reaches of the Yangtze River. A health assessment of a land use system can effectively guide the rational land use and coordinate the contradiction between urban development and natural ecological protection. This study proposes a health evaluation index system of a land use system based on a PSR (pressure-state-response) model. Through the improved TOPSIS method, this research conducted an empirical study of Chongqing as a typical example of health assessment of a land use system in the ecologically sensitive area of the Three Gorges reservoir area. The results showed that: 1) The score of the Three Gorges reservoir area land use displayed a pattern of the "T" zonal distribution, which can be categorized as healthy, critical, unhealthy, and morbid. Morbid and unhealthy regions mainly cover the northeast, the southeast, and the southwest of Chongqing, which are in the state of stress and have higher health index. The critical and healthy regions are located mainly in the loop of main urban area in Chongqing. 2) The ecosystems in the northeast, southeast, and southwest regions of Chongqing, which are in morbid and unhealthy conditions, belong to high risk-high pressure areas, because of their fragile and unstable ecosystems and high risks of land use. The loop area in the Chongqing urban area, which is at low risk of land utilization and in relatively good condition, is in the low risk-moderate pressure area. To foster healthy development of land use in the ecologically sensitive area in the Three Gorges reservoir area, land use planning and adjustment should be strengthened, excessive human development of land should be restricted, and the ecosystem functioning should be maintained. 3) The PSR model as a means of analysis and unifying the natural resources, the environment, and social economy, not only emphasizes the health condition of ecosystems but also considers the impact of socio-economic activities and their association in carrying out a comprehensive health evaluation of the land use system. PSR shifts the research focus to natural resources and environmental conditions. It fully characterizes the spatial characteristics of the land use system, accurately displays the relationship between various elements of a healthy land use system and the key factors affecting the ecosystem, and sets an early alarm for a land use system for the ecologically sensitive land in the Three Gorges reservoir area. 4) The improved TOPSIS method can make full use of original data, illustrate the reality, achieve a comprehensive diagnosis of the health condition of a land use system, and reveal the level of each indicator as well as the critical factors affecting the system. The method is effective and can be applied to other kinds of assessment with proper adjustments. 5) The evaluation index system based on the PSR model and the improved TOPSIS method can be applied to health assessment of a land use system. Both analysis methods can enhance the health condition of a land use system. This study can be a reference for further improvement of a health assessment of land use as well as for land use planning, management, and ecological protection.