Abstract: It is of great significance to measure the green total factor productivity of Chengdu-Chongqing economic circle, analyze the regional differences, and explore its influencing factors and spillovers, which will promote the green transformation. The panel data of 16 prefecture-level cities in Chengdu-Chongqing economic circle from 2004 to 2021 were selected to calculate green total factor productivity (GTFP) by using Super-SBM model considering non-expected output, and the spatial Durbin model was constructed to explore the spatial effects of different factors. The results show that: (1) GTFP presents an unstable and fluctuating state, forming an obvious spatial feature of “high in the middle and low in the wings”. (2) Through the Moran’s I, it shows a positive spatial correlation. (3) Economic development and industrial structure can increase GTFP, while other variables can inhibit GTFP. (4) Further analysis shows that economic development only has a significant promoting effect on GTFP in the region; industrial structure can promote GTFP both locally and in neighboring areas; the level of urbanization and the size of the city have a significant inhibitory effect on the local area; the area of green space has a significant inhibiting effect on the local area, but a significant promoting effect on the neighboring area.