[Objective] The spatiotemporal interactive coupling characteristics between mountainous urbanization and ecosystem health, and the complex relationship between ecosystem health and urbanization were studied to provide a scientific basis for the scientific management and sustainable development of urban areas in the region. [Methods] The spatial and temporal evolution characteristics of urbanization and ecosystem health subsystems were analyzed for Chongqing City (a mountainous city) from 2000 to 2020 using the entropy value method and the vigor-organizational-resilience-service (V-O-R-S) model to determine the mechanism of the interactive coupling relationship between urbanization and ecosystem health subsystems. [Results] ① The comprehensive urbanization level in Chongqing City from 2000 to 2020 increased year by year. However, there was still a problem of uneven spatial development, and both the core zone and the low-value area were significantly affected by topographic relief. ② The ecosystem health index from 2000 to 2020 was moderate. The ecosystem health of the regions with rapid urbanization deteriorated significantly, while the ecosystem health of Southeast Chongqing and Northeast Chongqing with higher vegetation cover was good. [Conclusion] The interactive coupling between urbanization and ecosystem health subsystems was on the rise, but has not yet reached a highly coordinated stage, and contradictions still exist. To achieve high-quality and sustainable development in Chongqing City, it will still be necessary to take the green development path and solve the problem of spatial and temporal inequality.