Ecological compensation is a critical strategy that can be used to promote regional cooperation for the improvement of air pollution control. Overall, this study considers the relationship between air pollution production and economic growth; through this, we incorporate elements such as ecological compensation, technological progress, and PM2.5, into the framework of sustainable development theory. Under the constraints of the air pollution control objectives, a dynamic computable general equilibrium model was constructed to analyze the efficiency of air pollution control and responsibility allocation in the Yangtze River Delta region. Overall, this study yielded several findings. First, with each 10 billion yuan allocated for ecological compensation in the Yangtze River Delta region, there was an annual average carbon emission reduction of approximately 0.26%; this equated to an annual total carbon emission reduction of approximately 8.3 million tons per 10 billion yuan of ecological compensation. Additionally, the annual average PM2.5 concentration was determined to reduce by 0.72 μg/m3 per 10 billion yuan of ecological compensation; this indicated that effective ecological compensation can lead to a significant improvement in air pollution control. Second, the initial allocation of ecological compensation was distributed in the following order, from the highest to lowest burden: Jiangsu, Zhejiang, Anhui, and Shanghai. Third, we calculated the responsibility for air pollution control; this indicated that local contributions to the inter-regional external transmission of air pollution by the Jiangsu, Zhejiang, Shanghai, and Anhui regions were 65%, 62%, 53%, and 84%, respectively; in contrast, the external contributions to their surrounding regions were 35%, 38%, 47%, and 16%, respectively. Overall, Anhui possessed a higher responsibility for internal responsibility transfers among Jiangsu, Zhejiang, and Shanghai, highlighting the role of Anhui in the fossil fuel industry within the Yangtze River Delta region. Finally, the present study established that there were significant variations in the redistribution of ecological compensation among provinces and cities within the Yangtze River Delta region. Redistribution lead to a reduction in ecological compensation by approximately 1/4 in Zhejiang and Shanghai and approximately 4% in Jiangsu; conversely, this redistribution nearly doubled the ecological compensation allocated to Anhui. Overall, the appropriate allocation of responsibility pertaining to internal trade transfers (i.e., fossil fuels trade) in air pollution and inter-regional external transmission (i.e., air spillover) is crucial for effective air pollution control in the Yangtze River Delta region and other parts of China and, therefore, requires immediate attention.