Based on the cityscape data of 108 cities from 2004 to 2014, the paper analyzes the spatial and temporal pattern of urban eco-efficiency in the Yangtze River economic zone. In conclusion, the ecological efficiency level of the Yangtze River economic belt shows a fluctuating trend, and the urban ecological efficiency differentiation characteristics of the Yangtze River Basin are obvious. The ecological efficiency of the upper reaches of the Yangtze River in Hunan, Hubei and Sichuan is higher, and the urban ecological efficiency of the upper, middle and lower reaches of the Yangtze River is decreasing. The research on the influencing factors of ecological efficiency shows that technological innovation has significantly improved the ecological efficiency of the Yangtze River economic belt. The rapid economic growth has reduced the ecological efficiency of the city, which means that changing the mode of economic growth and accelerating scientific and technological innovation is an effective way to improve the ecological efficiency of the city. It is found that industrial structure deviation is beneficial to the improvement of urban ecological efficiency, and industrial upgrading restrains the growth of urban ecological efficiency from the rationalization of industrial structure and the construction of industrial upgrading index. This also means that industrial upgrading is not a shortcut to improving urban eco-efficiency.