Abstract: Due to the regional resource endowment differences along the Yangtze River, uneven distribution of industries, large income gap and so on. This leads to the differences in the path, space, time and degree of different pollutants in the production process of different regions along the Yangtze River. Then, regional differences will occur when exploring the linkage between the economy and environment along the river, so there are various forms of EKC in different regions. Based on the panel data of 45 cities along the Yangtze River from 2003 to 2018, this paper selects five single environmental indexes from the five environmental levels (atmosphere, water, sound, soil and biology), and constructs a comprehensive environmental index. The traditional EKC and SDM models are set according to the characteristics of environmental indicators .Relying on the comparison of single and comprehensive environmental index EKC curve, this paper classifies the cities along the river by defining the scope of the basin and dividing the level of economic development, and studies the internal linkage between economic growth and environmental quality. The results show that: (1) There are limitation and instability in measuring environmental quality by single environmental index. When the per capita industrial sulfur dioxide emission, per capita industrial waste water emission and urban road noise are taken as the environmental quality indicators, the economic growth and environmental quality present a "U" curve. However, when comprehensive environmental indicators are used, they are inverted "U" type. At the same time, each index shows different degrees of spatial spillover effect, and the most significant spillover effect is industrial wastewater. (2) The environmental governance of cities along the Yangtze River lacks the overall situation, and the scope of governance needs to be expanded. In recent years, the emission reduction effect of industrial sulfur dioxide and industrial wastewater is remarkable, but the green coverage rate of the built-up area and the comprehensive utilization rate of industrial solid waste show a slow downward trend at this stage. (3) Due to the heterogeneity of samples, the linkage relationship between comprehensive environmental indicators and economy presents a variety of forms: the upstream area is inverted “U” type; the middle and high-income area is positive “U” type; the downstream area is “W” type; low-income areas are of the “M” type. It is found that the environmental problems in the downstream areas are more prominent and need to be rectified, and the low-income areas should take preventive measures, take active measures and control ahead of time.