Achieving sustainable development that harmonizes environmental protection with economic growth in the Yangtze River Economic Belt (YREB) remains a critical area of research. Examining green total factor productivity (GTFP) aids in pinpointing the key factors and pathways essential for fostering green economic development. On the basis of 108 prefecture-level cities in the YREB, a three-stage SBM-ML index model was constructed to measure the GTFP level from 2009 to 2022. ArcGIS software was used to analyze the spatiotemporal evolution of GTFP dynamically. Finally, the multidimensional factors affecting GTFP were systematically analyzed via the Tobit model. The study revealed that (1) GTFP exhibits notable spatial disparities among the upper, middle, and lower reaches of the YREB, with the downstream areas showing higher levels than the upstream and midstream areas do. (2) After excluding environmental factors and random errors, the true GTFP level significantly decreases, indicating a notable environmental masking effect, with a masking effect of up to 63.9%. (3) The spatial distribution of GTFP overall shows a “low-high-low-high” pattern from west to east, forming an “N”-shaped spatial pattern. (4) The Tobit model regression results show that government governance enhances GTFP, while economic growth and intergovernmental fiscal decentralization hinder real GTFP. Although urbanization was initially insignificant, it significantly boosted real GTFP post-COVID-19. Finally, policy recommendations to promote green development in river basins are proposed.
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