From October 2013 to July 2015, composition and seasonal succession of phytoplankton functional groups in Lake Taihu were investigated during different seasons. During the survey, 20 functional groups were identified with the predominant groups in the succession of M, Y, C, J, P, S1, D, H1, T, MP and W1. Functional groups composition in Lake Taihu demonstrated obviously seasonal dynamics, and the M, C and Y functional groups had higher proportion in each season. Redundancy analysis showed that the distribution of functional groups dominated by M and C functional groups in summer and autumn was mainly affected by transparency, and the distribution of functional groups dominated by Y functional groups was mainly affected by total nitrogen concentration. Pearson correlation analysis showed that there was a significant positive relationship between Q index and Shannon-Wiener index with water temperature and ammonia nitrogen, and there was also a significant positive correlation between the two water quality assessment methods. Comparing the Q index, Shannon-Wiener index and the TLI index, we found that the Q index evaluation method can better reflect the nutritional status of the water body. Above all, this study shows that functional groups can directly reflect the seasonal succession characteristics of phytoplankton in Lake Taihu, and can objectively indicate the water quality of Lake Taihu.