Taihu Lake can be divided into several different lake regions such as bay area, center area, lakeshore area and etc. according to the hydrodynamic characteristics and the lake morphology. In the year of 2010, water quality were measured in 17 sampling points, consisting of 8 points in the Zhushan Lake bay, 3 points in the western lakeshore area, and 6 points in the center area. The fuzzy hierarchy comprehensive evaluation model was used to assess the water quality in different lake regions on the basis of the measured data. This method is a combination of fuzzy evaluation to determine membership degree and Analytic Hierarchy Process (AHP) to determine weight. AHP can be further reduced to these steps such as the goal defining, hierarchy establishing, judgment matrix building, hierarchy single ranking, hierarchy general ranking and uniformity inspecting. The results show that water quality of Zhushan Lake bay is in class Ⅴ except for some points in class Ⅳ. Water quality of center area is between class Ⅱand Ⅳ, and that of lakeshore area is in class Ⅴ. The water quality assessment on the different lake regions by this method can more practically reflect the water environmental status of Taihu Lake. This works contributed to the improvement of water quality assessment exactness and lake eutrophication controlling in the situation of the lake with large area.