In recent years, as one of the old industrial bases in China, although it has been promoting the construction of new industrialization, Chongqing is still facing a more severe situation of industrial pollution. In order to further upgrade the optimization of industrial structure in Chongqing, the paper combined with 2773 cases of Chongqing pollution administrative penalties. Select industrial pollution enterprises administrative penalty amount of the 38 districts and counties in Chongqing as cross-sectional data, the spatial correlation of industrial pollution in Chongqing was analyzed by exploratory spatial analysis. Then, using the coupled coordination degree model, the evaluation index system of economic development and industrial pollution coupling degree in Chongqing area is established, and the spatial pattern of the economic environment coupling degree in Chongqing is analyzed. It is found that the spatial agglomeration characteristics of industrial pollution in Chongqing are not obvious, and the regional pollution is different, the economic environment system is in the state of low coupling, the spatial types of the coupling degree of regional economic environment are the most antagonistic economic environment, and the minority is the low coupling region. Based on the results of spatial layout, this paper analyzes the industrial structure of Chongqing City and put forward the optimization strategy of industrial structure.