Since the reforming and opening-up of China in 1980s Taihu basin has witnessed great progress in social-economic development and economic restructuring as well as the deterioration of water environment.The paper focuses on the change of manufacturing structure and its impacts on the water environment in the Suzhou-Wuxi-Changzhou District.It is showed that there exists certain relationship between the change of industrial structure and TP and COD in Taihu Lake especially the manufacturing structure change in the past 20 years.It is urgent to make adjustments to industry structure and reform pattern of economic development to protect water environment in Taihu Lake basin.The paper also gives some suggestions about the studying on the relationship between industry structure and water environment in the future.