To correctly understand the relationship and coordination degree among technological innovation, industrial structure and ecological environment, a three-system two-level index evaluation system was constructed. Based on coupling coordination model, temporal evolution and spatial difference evolution of coupling coordination of three major systems in 11 provinces and cities of Yangtze River economic belt from 2009 to 2017 were analyzed using entropy value method. The results showed that the full-time equivalent of R&D personnel, per capita GDP and general industrial solid waste production contributed highly to technological innovation, industrial structure and ecological environment. The comprehensive evaluation indices of three systems all had interprovincial differences, and the degree of innovation was positively correlated to industrial structure optimization, while negatively correlated to ecological environment. Temporally, the level of coupling degree of three systems from 2009 to 2017 was relatively high and interannual differences in some areas changed greatly, while the degree of coupling coordination was low and interannual difference change was small. Spatially, coupling degree and coupling coordination degree of provinces and cities in the region were different obviously and showed agglomeration trend. The coupling degree of each province and city basically reached high-level coupling stage, and coupling coordination degree was relatively low overall, showing the trend of high in the east and low in the west.