<p>Urban green development has become a major concern worldwide, especially in urban agglomerations where regional integration is deepening. Yet empirical evidence on how regional integration (INT) shapes green development in such areas remains limited. Using panel data for 41 cities in the Yangtze River Delta Urban Agglomeration (YRDUA) over 2006–2020, this study investigates the spatiotemporal dynamics of INT and green total factor productivity (GTFP) and explores the channels through which INT affects GTFP. The results yield four main findings. First, both INT and GTFP exhibit significant positive spatial dependence within the YRDUA. Over time, INT increases steadily but remains unevenly distributed across cities, whereas GTFP shows an increasingly pronounced core-periphery divide. Second, the relationship between INT and GTFP is U-shaped: INT begins to promote GTFP only after passing a turning point, which has already been exceeded by most cities in the YRDUA. Third, INT improves GTFP by expanding market size, optimizing industrial structure, and stimulating green technological innovation. Threshold analysis further identifies the ranges within which these mediating channels operate most effectively. Fourth, the effect of INT is positive in central cities, where all mediating channels work in the expected direction. By contrast, in peripheral cities, INT suppresses GTFP, with industrial structure optimization serving as the only channel that partially mitigates this adverse effect. Using the expansion of the Yangtze River Delta City Economic Coordination Committee as a quasi-natural experiment, a staggered DID analysis further corroborates the heterogeneous effects of INT on GTFP between central and peripheral cities. Overall, the findings deepen understanding of the environmental consequences of regional integration and inform differentiated green development strategies for cities within urban agglomerations.</p>