In the context of carbon emissions peak, environmental issues highlight the importance of the green economy, how does economic agglomeration release growth potential and enable the coordinated development of the economy and environment? There are few works of literature to analyze it within the framework of spatial economy. This paper constructs a theoretical model to clarify the influence mechanism of economic agglomeration on green total factor productivity (GTFP), and then uses a dynamic SDM model to test the theoretical hypothesis. This contribution has three main findings. First, there is a "U-shaped" curve relationship between economic agglomeration and GTFP, and the formation mechanism is that economic agglomeration has a threshold effect on the agglomeration externalities such as infrastructure sharing, knowledge spillover, and labor market upgrading. Second, the mismatch of industrial structure is an important reason that the economic agglomeration in this region has not produced an obvious spatial spillover effect on other regions; Relaxing restrictions on the concentration of economic activity to regional centers would contribute to the improvement of GTFP. Third, GTFP has the classic "snowball effect" in the time dimension, but has the obvious "warning effect" in the space and time dimension. Based on this, this paper believes that at the present stage, it is necessary to adapt to the layout of economic geography, promote the rational allocation of human resources in the territorial space, promote the coordination between economic agglomeration and the development goal of green economy, and at the same time, it is necessary to cultivate the cooperative linkage mechanism of green economy development and transformation among cities.