Abstract: The rapid development of cities impacts the health of regional ecosystem, while ecosystem health is the foundation supporting the sustainable development of urbanization. Currently, most studies focus solely on the overall relationship between urbanization and ecosystem health, and few studies explore the coupling coordination relationship and spatio-temporal heterogeneity between the two subsystems. Therefore, in this study, the coupling coordination degree model (CCDM) and the geographically and temporally weighted regression model (GTWR) were mainly used to measure the coupling coordination relationship between urbanization and ecosystem health in Chengdu-Chongqing economic circle from 2000 to 2020, as well as the spatiotemporal heterogeneity between the two subsystems. The research showed that: (1) From 2000 to 2020, the urbanization level of the study area gradually increased, but there was still the problem of uneven spatial development. (2) The ecosystem health index showed a trend of initially rising and then declining, and the overall level was at a medium level. The spatial distribution featured high values around the periphery and low values in the center. (3) The level of coupling coordination degree between urbanization and ecosystem health was basically coordinated, which gradually increased with time, and the spatial distribution was uneven, with Chengdu and Chongqing as bipolar cores. (4) The spatio-temporal heterogeneity distribution of the two subsystems was quite different, in which the positive effects were mainly concentrated in the central area of the study region, and the negative effects were mainly in the surrounding areas. This study aims to provide scientific reference for the high-quality, green, and healthy development of the Chengdu-Chongqing economic circle.