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In the context of significant environmental changes, the urgency of adopting green innovation has become increasingly apparent as a central mechanism for adjusting industrial structures in China. This transition serves not only as a crucial way to address pressing environmental challenges, but also as a fundamental strategy to improve the ecological efficiency of urban areas. Existing research mainly keeps a close eye on the unidirectional relationship between variables such as technological innovation and environmental protection. There is less relevant literature that has researched the cointegration relationship among green innovation, industrial structure, and eco-efficiency of cities. The essential role of green innovation and industrial structure in reaching a higher eco-efficiency of city are discussed in this research and the relationship among these three variables are analyzed by the evidence from cities in China from 2011 to 2019. The fact that the variables are cointegrated in the long run is evidenced by the results for the full sample. The sub-sample results report that in the eastern region, green innovation, industrial structure upgrading, and industrial structure rationalization could improve urban eco-efficiency. However, in Midwest regions where economic development is relatively backward, green innovation's effect on urban eco-efficiency is not in a significant positive way. The results obtained in this paper have implications for different cities in China to formulate corresponding policies on green innovation, industrial structure, and urban eco-efficiency. [ABSTRACT FROM AUTHOR]