Green innovation is an important driving force to promote the sustainable development of urban society and economy. This paper constructs an evaluation index system containing social undesirable outputs, and uses the Super-SBM model and the Malmquist-Luenberger index to evaluate green innovation efficiency in 42 cities along the Yangtze River Economic Belt from 2013 to 2017. Additionally, spatial autocorrelation analysis is used to study the spatial correlation of green innovation efficiency. Finally, the coupling coordination degree model is used to study the coupling coordination degree between green innovation efficiency and high-tech industries. The following results were obtained. (1) The average value of green innovation efficiency increased from 1.0446 to 1.0987, and the annual average growth rate of total factor productivity of green innovation was 1.1%. (2) Green innovation efficiency of the Yangtze River Economic Belt had a significant spatial positive correlation, but the types of agglomeration among cities in different sections of the Yangtze River were quite different. (3) The coupling coordination degree between green innovation efficiency and the development level of high-tech industries in the cities of the Yangtze River Economic Belt was in the basic coordination stage. Based on the research results, we suggest that cities in this belt further enhance the interactive relationship between green innovation and economic development and promote the coordinated development of economy and society.