Abstract: The rapid development of cities impacts the health of regional ecosystems, while ecosystem health is the foundation supporting the sustainable development of urbanization in the region. Currently, most studies have focused solely on the overall relationship between urbanization and ecosystem health, with few exploring the coupling coordination relationship and spatiotemporal heterogeneity between their subsystems. Therefore, this study primarily employed the Coupling Coordination Degree Model (CCDM) and the Geographically and Temporally Weighted Regression Model (GTWR) to measure the coupling coordination relationship between urbanization and ecosystem health in the Chengdu-Chongqing economic circle from 2000 to 2020, as well as the spatiotemporal heterogeneity between their subsystems. The research findings indicate: 1) From 2000 to 2020, the level of urbanization in the study area gradually increased, but there were still issues of uneven spatial development. 2) The ecosystem health index showed a trend of initially rising and then declining from 2000 to 2020, remaining at a moderate level overall. The spatial distribution featured high values around the periphery and low values in the center. 3) The coupling coordination degree between urbanization and ecosystem health was at a basic coordination level, gradually increasing over time, with uneven spatial distribution, presenting a layered distribution centered around the dual poles of Chengdu and Chongqing. 4) The spatiotemporal heterogeneity of the subsystems showed significant differences, with positive effects mainly concentrated in the central area of the study region, while negative effects dominated the surrounding areas. This study aims to provide scientific references for the high-quality, green, and healthy development of the Chengdu-Chongqing economic circle.