Urban agglomerations are not only the core areas leading economic growth but also the fronts facing severe resource and environmental challenges. This paper aimed to increase our understanding of urban eco-efficiency and its influencing factors and thus provide the scientific basis for green development. We developed a model that incorporates super-efficiency, slacks-based-measure, and global-frontier technology to calculate the total-factor eco-efficiency (TFEE) and used a spatial panel Tobit model to take into account spatial spillover effects. An empirical study was conducted utilizing a prefecture-level dataset in the Yangtze River Delta Urban Agglomeration (YRDUA) from 2003 to 2016. The main findings reveal that significant spatial differences exist in TFEE in the YRDUA: high-TFEE cities were majorly located in the coastal areas, while low-TFEE cities were mostly situated inland. Overall, TFEE shows a trend of “decline first and then rise with fluctuation”; the disparity between inland and coastal regions has expanded. Further regression analysis suggests that industrial structure, environmental regulation, and innovation were positively related to TFEE, while foreign direct investment was not conducive to the growth in TFEE. The relationship between population intensity and urban eco-efficiency is an inverted U-shaped curve. Finally, several specific policy implications were raised based on the results.
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