Abstract: Water pollution is one of the important problems of water environment in Taihu Lake basin. To evaluate the water quality of the watershed exactly and reasonably is vital to grasp the characteristic of water pollution and water environmental management. Single-factor identification index was used to evaluate the pollution status of a single element of typical sections. The original and the improved methods of comprehensive identification index and grey incidence analysis based on pollutant weight were used to evaluate the integrated water quality from 2004 to 2013. The analysis results show that the water pollution of east and southeast in Taihu Lake basin was more serious and the main pollutant was NH3-N, which was in accordance with the situation of eutrophication, so the leading management was to reduce the water eutrophication. There were some differences among the results of different water quality evaluation methods, which could reflect the water quality in Taihu Lake basin. The results of comprehensive water quality identification index and grey incidence analysis preferred the lower quality, and those of the improved comprehensive water quality identification index combined with the influence of the worst pollutant preferred the integrated water quality to overcome the error caused by the algebraic average of a single index in order to reflect the pollution of watershed veritably.