Abstract: The study illustrated phytoplankton community structure at 18 estuaries of Lake Taihu and assessed their ecological conditions according to index of biotic integrity based on phytoplankton (P-IBI). Samplings were conducted seasonally from May 2018 to March 2019. A total of 119 phytoplankton species belonging to 7 groups and 66 genera were identified. The mean phytoplankton density and biomass was 8.91×10⁶ L^-1 and 1.46 mg·L^-1, respectively. At seasonal scale, the total density and biomass reached the maximum value in summer (2.35×10⁷ L^-1 and 4.06 mg·L^-1, respectively), and the minimum values were in winter (3.84×10⁵ L^-1and 0.36 mg·L^-1, respectively). In terms of morphologic functional groups, Group Ⅲ and Ⅶ had higher biomass in summer (0.18 mg·L^-1 and 0.04 mg·L^-1, respectively). Phytoplankton density, Chlorophyll a and Menhinick were selected to establish P-IBI. Generally, the ecological condition in main estuaries was "low", and the average P-IBI value was 42.64. Spatially, "low" was the dominated condition (accounting for 55.56% of all sampling sites), followed by "moderate", and 2 sampling sites were classified as "bad". At seasonal scale, the maximum and minimum average P-IBI value was in winter (53.15) and summer (27.59), respectively. The water ecological condition was "low", "low", "moderate", and "moderate" in spring, summer, autumn and winter, respectively. The Spearman correlation analysis show that the P-IBI was significantly and negatively correlated with water temperature, pH and permanganate index (P < 0.05), and significantly and positively correlated with nitrate (NO₃^--N) (P < 0.05). There is also a good agreement between P-IBI and the Ⅲ and Ⅶ biomass that characterize harmful algae.