The author of this paper analyzed the water quality monitoring data, of Taihu lake from 2000 to 2005,getting the average value of water quality in different areas. The grey clustering method was used to evaluate the water quality of different lake areas, and the relative progress degree of seasonal variation of water quality in different lake areas was calculated by using Markov model. The results show that spatial and temporal differences of water quality in Taihu Lake is obvious: the water quality of Zhushan Lake and Meiliang Bay is worst, the water class is Ⅴ,but the water quality of east Taihu Lake and eastern of Taihu Lake is relatively better, the water class is Ⅱ. Among different water quality indicators, the degree of spatial heterogeneity of ammonia nitrogen is the largest, followed by the total nitrogen and total phosphorus, while the degree of permanganate index is relatively smaller. The results indicate that sewage is the main source pollution of Taihu Lake. The seasonal variation of water quality in Zhushan Lake and Meiliang Bay is the largest, and the water quality in summer and autumn is relatively better than that in winter and spring. While the seasonal variation of water quality in the other lake areas is small.