Abstract: The in-depth implementation of the Development Strategy of the Yangtze River Economic Belt cannot be separated from the coordinated development and common progress of scientific and technological innovation and green development. Based on the perspective of urban agglomeration, taken 85 cities in the three major urban agglomerations of the Yangtze River Economic Belt from 2010 to 2019 as the research object, employed the entropy weight method, the super-efficiency SBM model, the coupling coordination degree model and the Tobit model, discussed the coupling coordination relationship and spatial-temporal evolution characteristics between scientific and technological innovation and ecological efficiency, and analyzed the key impact factors of coupling coordination degree. The results showed that: (1) From 2010 to 2019, the overall scientific and technological innovation level of the Yangtze River Economic Belt presented a steady rising trend, while the variation trend of the ecological efficiency level exhibited a W-shaped with a “descending - ascending - descending - ascending” feature. The coupling coordination degree of scientific and technological innovation and ecological efficiency showed a fluctuating upward trend with an inverted U-shaped pattern. The spatial heterogeneity between the three major urban agglomerations were significant, which exhibited that the Yangtze River Delta urban agglomeration > the middle reaches of the Yangtze River urban agglomeration > the Chengdu-Chongqing urban agglomeration. (2) There was a significant spatial autocorrelation feature between the overall coupling and coordinated development level, and most cities showed low and low agglomeration. The Yangtze River Delta urban agglomeration showed a significant “high in the east and low in the west” spatial agglomeration , while the middle reaches of the Yangtze River urban agglomeration and Chengdu-Chongqing urban agglomeration had no significant spatial agglomeration characteristics.(3) The level of economic development , the agglomeration of the labor force , the opening-up degree and the industrial structure had a significant positive impact on the overall coupling coordination level of the Yangtze River Economic Belt. Based on the above conclusions, this study puts forward suggestions for strengthening the ecological environment protection of the Yangtze River Economic Belt, emphasizing the heterogeneity of regional development, introducing and cultivating innovative talents, and actively carrying out open exchanges with the outside world.