Abstract: Under the background of the “double carbon” goal, the green transformation of the manufacturing sector is a crucial factor to realize carbon peak and carbon neutrality goals. Since basins are essential support for the construction of ecological civilization, this paper measured the efficiency of green transformation of the manufacturing industry based on the panel data of 21 provinces (cities and districts) in the Yangtze River, Yellow River, and Pearl River basins from 2006 to 2020, using the undesirable super-efficiency SBM model. This paper made a multi-level comparison of the green transformation efficiency in the above three river basins from the perspective of efficiency level, dynamic change, and variance analysis. Furthermore, we analyzed the influencing factors of the green transformation of the manufacturing industry. This research demonstrated a fluctuating upward trend in the manufacturing industry’s green transformation efficiency. Additionally, the issue of uneven green manufacturing industry efficiency was detected between river basins, with the Yangtze and Pearl River basins having higher levels of green manufacturing efficiency than the Yellow River basin. Human capital variables were not found to have substantial impacts on the efficiency of the green transformation of industrial businesses, however, the level of urbanization, environmental restrictions, and foreign investment were identified to have significant impacts. Based on the above outcomes, countermeasures and suggestions were put forward to increase the manufacturing sectors’ green transformation efficiency in the three river basins.