Using principal component analysis method in SPSS 20.0 statistical software, the data of 28 water quality indexes in 9 level Ⅲ aquatic ecological function zones in the Lake Taihu basin as well as in each lake region were separately processed. Five principal components from the original monitoring data were derived. According to the contribution rate and score of each principal component, the combination of main pollution factors and relative pollution sources were analyzed finally. The first principal component reflected the key factors of the water eutrophication including N and P. The second principal component reflected the heavy metal matter level. There existed a significant spatial pattern in pollution source characteristics, and water quality both in basin and lake deteriorated not only from the south to the north, but also from the east to the west. The results indicated that exogenous source was a key factor causing water pollution in Lake Taihu. This study provides important information and foundation for the environmental monitoring and pollution treatment.