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This paper utilizes an improved undesirable output DEA model to measure the eco-efficiency of cities in five major urban agglomerations in China during 2006–2020. It employs the Theil Index and Geodetector to investigate the spatial-temporal distribution differentiation characteristics and driving factors of urban eco-efficiency. The main findings are as follows. Firstly, the eco-efficiency of all urban agglomerations showed a fluctuating upward trend, but the eco-efficiency performance of different urban agglomerations in China shows a stratification characteristic. Specifically, the Pearl River Delta urban agglomeration consistently ranks first in China, while the mean values of the Yangtze River Delta urban agglomeration, Beijing-Tianjin-Hebei urban agglomeration, and Chengdu-Chongqing urban agglomeration are lower than the national average. Secondly, the overall differences in the urban eco-efficiency of all sample cities show a consistently fluctuating downward trend. The factor that affects the level differences of eco-efficiency in different cities is the intra-regional differences. Last but not least, the top three factors affecting the spatial distribution difference of urban eco-efficiency in the whole sample are environmental pollution control investments, innovation level, and environmental infrastructure investments. In the end, this paper proposes that reducing the intra-regional differences is the primary task to achieve the coordinated improvement of urban eco-efficiency in urban agglomerations, and then puts forward some policy suggestions to improve eco-efficiency for the five major urban agglomerations. [ABSTRACT FROM AUTHOR]