The scientific measurement of regional atmospheric environmental efficiency is an important prerequisite for achieving energy conservation and haze reduction and regional green and high-quality development. Taking the cities in the Yangtze River Delta region from 2012 to 2021 as the research object, the atmospheric environmental efficiency is measured from both static and dynamic perspectives using the three-stage DEA model and the Malmquist index to analyze the characteristics of spatial and temporal differences. The study finds that the real atmospheric environmental efficiency of the Yangtze River Delta region is 0.915, and the elimination of environmental factors and random errors is crucial to the assessment of the efficiency. The atmospheric environmental efficiency of the Yangtze River Delta region is not 1, and there is still room for improvement, in which the pure technical efficiency is the main factor that leads to the overall low efficiency. Different environmental variables have different impacts on the atmospheric environmental efficiency, in which the positive impact of the industrial structure is the most significant. Urban agglomerations can be categorized into “high–high–high”, “high–low–high”, “low–low–high”, and “low–high–low”. The total factor productivity of the atmospheric environment showed a gradual growth trend during the study period, in which technological progress played the most important role. Based on this, countermeasures are proposed to better enhance the level of atmospheric environment management in the Yangtze River Delta region.
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