Taihu Lake basin is a typical water shortage area for water quality problem in China. Studying the influencing water environment factors in this area provides a scientific basis to propose effective pollution water control. This article selects lakes in the western basin as the study area which has the largest contribution to the pollution in Taihu Lake. Influencing factors of water pollution of Tianmuhu Lake and Gehu Lake have been analyzed based on principal component analysis of SPSS, to study the major influencing factors of water environment. The results show that the major influencing factors of water environment in Taihu Lake is dissolved oxygen, water turbidity, and water N, P and other nutrient elements, and the water environment nutrients is much influenced by the N element. While the major influencing factors of water environment in Gehu Lake is P nutrition elements, physical and chemical factors and nutrients such as N and P element, and P elements are seriously polluted. Thus, the corresponding countermeasures should be forward according to different water characteristics during the process of water Pollution Control at the basin.