Land use change profoundly influences the regional ecosystem. Due to the increase of the human activity intensity and social demand, the negative impacts on the ecosystem health will last for a long time. Simulating the change of ecosystem health caused by land use change under multi-scenario is significant for regional land use patterns optimization and ecological security protection. However, previous studies have mainly focused on the influence of land use change on ecosystem structure or services, while few have explored and predicted its impacts on ecosystem health. In this study, taking Chongqing as the study area, we first analyzed the dynamic evolution characteristics of land use and ecosystem health in Chongqing from 2000 to 2020. Based on this, using the ecosystem health assessment model and the patch-generating land use simulation (PLUS) model, three scenarios (i.e., natural development (ND) scenario, ecological protection (EP) scenario, and urban development (UD) scenario) were performed to simulate the impacts of land use change on ecosystem health in 2030. The results show that: (1) From 2000 to 2020, the area of construction land increased, while the cultivated land area decreased, with the reduced land primarily transferring to forestland and construction land. The overall ecosystem health showed a positive trend but the regionally spatial distribution was significantly different. The level of ecosystem health in the northeast and southeast regions was higher than in the southwest region. (2) The land use types were still mainly cultivated land and forestland by 2030, and the area of construction land for ND scenario, EP scenario, and UD scenario increased significantly, with the increase of 63.59%, 44.54%, and 100.13%, respectively. The central urban area in the southwest would become the area of construction land expansion. (3) Compared with those in 2020, the ecosystem health values of ND scenario and UD scenario showed a declining trend. The expansion of construction land area and the reduction of forestland area were important factors contributing to the degradation of ecosystem health in those scenarios. However, EP scenario showed an increasing trend, which was contrary to the results that reflected the elasticity of the response of ecosystem health to land use change. Therefore, land use optimization under EP scenario was effective for the sustainable development of regional ecosystem health. In summary, the estimation of the impacts of land use change on ecosystem health with the coupling multi-model could provide valuable references and decision-making support for ecosystem protection management and land use policy optimization in the study area.