Water environment protection was one of the most important priorities in Taihu Basin, resulting in the importance of water environment evaluation. It was used to evaluate water quality of Taihu Basin by three methods of single factor index, comprehensive identification index and improved comprehensive identification index, including dissolved oxygen (DO), permanganate index (CODMn) and ammonia nitrogen (NH3-N), which distributed in six typical water quality monitoring sections. Results show that the main pollutant is NH3-N in Taihu Basin, especially Qingpu and Jiaxing, which indicate the main managements are to reduce the eutrophication and blue algae blooming. Comparison of these evaluations, the results of improved comprehensive identification index are reliable to the true condition of water environment.