The green transformation of the manufacturing industry is crucial for high-quality development of the Yangtze River Economic Belt, and environmental regulation and technological innovation may play key roles. Considering the undesirable output of the manufacturing industry, this paper adopted the undesirable-SE-SBM Model to measure the green transformation efficiency, which can reflect the core transformation performance. On this basis, this paper respectively adopted system generalized method of moments (SYS-GMM) and differential generalized method of moments (DIF-GMM) to explore the driving factors of green transformation, which fully considered the lag variable of transformation efficiency. The estimated results of green transformation showed that the efficiency of the Yangtze River Economic Belt has maintained an overall growth trend, while that of the eastern regions was higher than that of the central and western regions. The regional difference of transformation efficiencies showed a trend of convergence first and then expansion, however, a few regions such as Chongqing have achieved leapfrog development. The estimated results of driving factors showed the first-stage lag affected the green transformation positively, while the second-stage lag had a significantly negative effect. The ratchet effect and cumulative effect led to the continued efforts on green transformation, however, the timeliness of policy might cause a rebound in practice. As mentioned in green paradox, the environmental regulation had a negative effect, which might bring compliance costs. The technology innovation level indeed promoted the green transformation of manufacturing, but the scientific research investment did not exert the expected positive effect, while the utilization of many research funds lacked market orientation. Economic development level had a negative effect on green transformation, and it would play a positive effect only if it reached a certain stage. The industrialization and urbanization affected the efficiency positively, and the external dependence degree had a significant negative effect. It was not clear whether foreign direct investment (FDI) brought a pollution haven or pollution halo effect. In view of these conclusions, local governments should strictly enforce environmental regulations, build the regional green innovation system, improve marketization of research funds, optimize the export structure, and promote new urbanization and new industrialization.

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Based on the input and output data of the 11 provinces and cities in the 2006-2016 Yangtze River Economic Belt, the article selects R&D personnel’s full-time equivalent nuclear R&D research expenditure as the input index, selects the number of patent grants as an indicator of acceptable output, water consumption and wastewater discharge. As a non-conforming output indicator, the EBM model considering undesired output is used to measure the water innovation efficiency of each province and city, and calculate the global Moran’I index value, and draw the Moran index map for 2006, 2009, 2012 and 2016. It is found that water use efficiency is generally on the rise, and there is significant spatial autocorrelation between regions. Shanghai, Jiangsu and Zhejiang have been at the frontier level of efficiency and have the positive correlation. Chongqing and Guizhou have negative correlations with neighboring provinces and cities. In order to more effectively improve the water innovation efficiency of the Yangtze River Economic Belt, in addition to paying attention to the development of the province and the city itself, it is also necessary to pay attention to the radiation belt actions of neighboring provinces and cities, and formulate differentiated water management measures.