Abstract: Enhancing regional market integration and augmenting ecological efficiency are crucial strategies for the advancement of regional economic quality and the cultivation of a low-carbon economy. A comprehensive dataset incorporating panel data from 41 cities in the Yangtze River Delta region was compiled. The dataset covered the period from 2009 to 2020. Subsequent empirical analyses were conducted to examine the impacts of market integration on ecological efficiency. System GMM, regulatory effect model, and threshold effect model were applied in this study. The findings indicated that market integration was beneficial for enhancing the ecological efficiency of the Yangtze River Delta urban cluster. The influence exhibited notable heterogeneity across different periods, regional characteristics, and market categories. The government's focus on eco-environment exerted a positive regulatory role on the relationship between market integration and ecological efficiency. Moreover, the optimization of the industrial structure served as a threshold effect amidst the dynamics of market integration's impact on ecological efficiency. Consequently, the optimization of the industrial structure and the intensification of the government's focus on the eco-environment constituted effective strategies for enhancing ecological efficiency. The sustained promotion of regional market integration is instrumental in bolstering the ecological efficiency of the Yangtze River Delta region and fostering coordinated environmental governance development.