Pollution control is the difficulty and pain point of ecological environment protection and green development in the Yangtze River Economic Belt，and high pollution industry’s agglomeration is the important inducement of environmental problems. Based on the panel data of provinces along the Yangtze River Economic Belt from 1999 to 2018，the pollution intensive industry category and its spatial-temporal evolution pattern are systematically identified by using pollution intensive index and weighted standard deviation ellipse method，and then the fixed effect model is used to explore the green economic effect of pollution-intensive industry agglomeration. The results show that：the depth of pollution intensive industrial agglomeration in the Yangtze River Economic Belt is weaker than the national level，the industrial structure is transforming towards green and low-carbon，and the transformation effect in the downstream area is particularly prominent；the pollution intensive industrial agglomeration areas in the Yangtze River Economic Belt are significantly different，the pollution production capacity in the middle and upstream areas is strong，and the center of gravity is moving to the southwest；the pollution intensive industrial agglomeration has a strong impact on the Belt’s economy in the short term，the green development ability can restrain pollution production and pollution diffusion，especially in the middle and upper reaches；the pollution intensive industry cluster has a long-term green transformation mechanism，the endogenous industry cluster and the orderly layout of the government lead to the reduction of pollution production capacity，and the green transition rate in the lower，middle and upper reaches increases gradually. To further improve the green development capacity of the Yangtze River Economic Belt，it’s necessary to strengthen the technical support of green transformation of pollution-based industries，optimize the supervision of expansion and migration of pollution-based production capacity，and speed the cultivation of green emerging industry.