The importance of ecological restoration in the Yangtze River Economic Belt has become increasingly prominent. It is urgent to control the pollution emission of manufacturing industry and other industries in order to achieve green sustainable development. Based on panel data of 108 cities in Yangtze River Economic Belt from 2003 to 2016，this report used panel regression model and threshold effect model to empirically analyze the impact of FDI and industrial agglomeration on manufacturing pollution. The results showed that FDI had a significant inhibitory effect on manufacturing pollution in Yangtze River Economic Belt on the whole，and the effects were different in different parts of the Yangtze River Economic Belt；the effects of FDI varied with the level of industrial agglomeration；and industrial agglomeration had a deteriorating effect on manufacturing pollution in Yangtze River Economic Belt. Based on the above findings，this report proposes measures such as continuous introduction of high quality FDI，rational planning of FDI introduction and layout，and effective control of manufacturing agglomeration，in order to effectively alleviate manufacturing pollution in the Yangtze River Economic Belt.