China aims to reduce its carbon emissions to achieve carbon peaking and neutrality. Measuring the carbon emission efficiency of three urban agglomerations in China, exploring their spatiotemporal characteristics, and investigating the main influencing factors are crucial for achieving regional sustainable development and dual carbon goals. Using the super-slack-based measurement (super-SBM) model, we calculated the carbon emission efficiency of the Beijing–Tianjin–Hebei (BTH), Yangtze River Delta (YRD), and Pearl River Delta (PRD) urban agglomerations from 2011 to 2021 and explored the spatiotemporal non-equilibrium characteristics of carbon emission efficiency and its influencing factors. The results indicated that: (1) Overall, the carbon emission efficiency showed an N-type trend, with the PRD having the highest average efficiency. Regional differences between the YRD and BTH regions gradually increased. (2) The efficiency hotspots shifted from the PRD to the YRD, whereas the cold spots were mainly concentrated in the BTH region. The variation in the standard deviation ellipse radius of carbon emission efficiency in the urban agglomerations was clear, and the spatial disequilibrium was significant. (3) Economic level and opening up had positive impacts on carbon emission efficiency, whereas energy intensity and industrial structure had negative impacts. The effects of population size, government intervention, and technological level varied among the regions.
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