As a significant manifestation of human activities influencing natural environment, rapid urbanization has enhanced economic prosperity while simultaneously posing threats to ecological quality. Beijing–Tianjin–Hebei (BTH), the core region of the Yangtze River Delta (CYRD), and the Pearl River Delta (PRD) stand as three major economic centers characterized by the highest level of urbanization in China, encompassing areas of heightened ecological sensitivity. Nevertheless, the ecological quality at the scale of urban agglomerations remains ambiguous, with many studies failing to develop a comprehensive and effective method for comparing diverse urban agglomerations. Consequently, this study integrates multi-source remote sensing data, including information on land cover and other socio-economic parameters, to construct the Ecological Quality Index (EQI) based on the “Function–Interaction–Pressure–Stability” (FIPS) framework. Through a stratified determination of indicator weights grounded in both objective importance and empirical knowledge, we mapped the spatiotemporal changes of EQI and analyzed the impact of urbanization on ecological quality in three urban agglomerations from 2001 to 2020. We determined the following: (1) The calculated EQI can further capture the nuanced details with better performance at both underlining the discrepancy of highs and lows of EQI and describing the spatial detail of urban agglomerations’ characteristics. (2) Substantial disparities in EQI and its changes are evident across different urban agglomerations. Notably, only the average EQI improves in PRD, while ecological degradation is prominent in specific regions, such as the southeastern plains of BTH area, along the Yangtze River, and around Shanghai in CYRD and central PRD. The CYRD exhibits the largest affected area. (3) Urbanization predominantly influences ecological quality through land cover transitions. In expansion areas, ecological deterioration is significantly more pronounced, constituting approximately 90% of the total area. (4) Despite significant urbanization, city-level analysis in CYRD reveals a better coordination between urban expansion and ecological protection, with a lower intensity of ecological degradation compared to urban expansion rates. Conversely, some cities in the BTH, despite modest urban expansion, exhibit substantial declines in ecological quality, highlighting the need for targeted policy interventions. In conclusion, this study elucidates the intricate relationship between urbanization and ecological quality, offering valuable insights for the development of targeted protection strategies and sustainable urban planning.
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