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With the shortage of resources and the increasingly serious environmental pollution in China, green innovation has become a sustainable competition for a region. The Yangtze River Economic Belt (YREB) strategy is one of the most important strategies for the sustainable development of China’s economy under the new normal. Green innovation plays a linking role in the resources exchange and trade flow in YREB, and it is also the foundation and guarantee to implement the YREB strategy. The global environmental pollution and the weak recovery of world economy make the traditional extensive economic growth model unsustainable. Sustainable economic growth should focus on the quality of development and its external costs to the environment. In order to implement the concept of sustainable development, the improvement of logistics ecological efficiency is related to the quality of ecological civilization construction. Therefore, it is of theoretical and practical significance to study the measurement, evolution, and driving factors of coordinated development level of regional green innovation system. This paper proposes a super-slack-based measure (super-SBM) data envelopment analysis (DEA) model to measure the green innovation efficiency of 11 provinces and cities in YREB from 2008 to 2017, mastering its spatial and evolutionary characteristics, and conduct empirical analysis on the influencing factors. The empirical results indicate that economic development, government support, and industrial structure upgrading are the leading forces to directly enhance the green technology innovation ability of cities in the Yangtze River Economic belt and play the core driving role of green innovation. To further enhance the capacity of urban green innovation in the Yangtze River Economic belt, we will increase the government’s support for green innovation, optimize the environmental governance model, promote the green upgrading of industrial structure, and enhance the enthusiasm of enterprises for green innovation.