The paper used the super-efficiency SBM model and Malmquist index to calculate the green innovation efficiency of 29 regions in China from 2008 to 2017, and found a growing trend of green innovation efficiency in China, with great room for improvement. The eastern region has the highest efficiency of green innovation, while the central and western regions have little difference in this regard. The Malmquist index and change index of technical progress in 29 provinces and cities in China averaged above 1, with technical progress serving as the main factor behind improved efficiency of green innovation in China. The change index of technical efficiency in some cities is less than 1, so it is necessary to improve the efficiency of resource allocation.