With the acceleration of new-type urbanization, how to realize the coordinated development between urbanization and eco-environment will be the central topic of the development of Yangtze River Economic Zone. 36 cities in the Yangtze River Economic Zone were studied, three indices were selected to build an eco-environment health evaluation system, including the pressure, status and restoration potential of ecological environment. An entropy-comprehensive evaluation model was established to comprehensively assess the eco-environment health of each city. The results indicate that the eco-environment level of 36 cities in the Yangtze River Economic Zone has obvious spatial difference, and the synthetic index of environment of the cities on the lower reaches of the Yangtze River is higher than those on the middle and upper reaches. According to the differences of various eco-environment indices of 36 cities in the Yangtze River Economic Zone, the 36 cities are divided into six types with the PCA ordination. Finally, the study analyzed the relationship between urbanization and the pressure, status, restoration potential of ecological environment to understand the eco-environment level differences of 36 cities in the Yangtze River Economic Zone under the background of urbanization with the correlation analysis method. The results show that urbanization and the eco-environment pressure exhibit exponential curve and the coupling characteristics of urbanization and eco-environment of cities on the upper, middle and lower reaches of the Yangtze River are different.