Urban agglomerations should meet the dual requirements of economic growth and green development, and there is currently an urgent need to improve the efficiency of green development. Therefore, we analyzed the impact of the Yangtze River Delta Urban Agglomeration (YRDUA) policy on the digital economy (DE) and green total factor productivity (GTFP) using the time-varying difference in difference model (DID). The marginal contribution of this study is an evaluation of the long-term effect of the YRDUA policy on green high-quality development. Based on the perspective of the “Porter Hypothesis”, this study examined the similarities and differences in the impacts of urban agglomeration on DE and GTFP. The results show that the policy promotes the urban DE index, but significantly inhibits urban GTFP. This means that the overall impact of urban agglomeration policy on green high-quality development in the Yangtze River Delta (YRD) is still in the “weak Porter Hypothesis” state, the technological innovation and efficiency improvement stimulated by urban agglomeration policies are not enough to significantly improve GTFP, and the “strong Porter Hypothesis” is not tenable. In addition, the heterogeneity analysis shows that the policy has a more obvious role in promoting the green high-quality development of central cities, large and medium-sized cities and innovative cities. The level of urban public service supply shows a threshold effect. When it develops to a certain scale, the urban agglomeration policy has significant positive impacts on both DE and GTFP.