The Belt and Road Initiative (BRI), as a Chinese-driven approach to fostering a community with a shared future for humanity, demonstrates China’s commitment to global responsibility through its promotion of green development. This study investigates the impact of BRI on the Green Total Factor Productivity (GTFP) of cities along its domestic route, using annual panel data from 2004 to 2018 and applying the difference-in-differences (DID) methodology. The findings reveal that: (1) The BRI has a significant positive effect on the GTFP of cities along its domestic route, with this result remaining robust even after addressing concerns related to endogeneity and other potential policy disruptions. (2) The improvement in GTFP is largely driven by advancements in scientific and technological innovation, an increase in foreign direct investment, and strengthened trade cooperation. (3) When examining regional heterogeneity, the GTFP growth effect is notably stronger in inland cities compared to coastal ones, with cities exhibiting heightened environmental awareness experiencing more pronounced improvements. (4) There is a clear positive interaction between the BRI and the development of Free Trade Zones (FTZs), which further accelerates GTFP growth. (5) Spatially, the BRI not only boosts the GTFP of cities directly involved in the initiative but also positively influences the GTFP of neighboring cities along the route. This study provides valuable insights for policymaking and offers a theoretical foundation for advancing the green development agenda of the Belt and Road, supporting China’s efforts toward sustainable economic growth and high-quality transformation.