Suzhou is one of the central cities in the Yangtze River Delta, which has recently been facing increasingly serious eutrophication-related problems in the river courses in its urban area. To investigate the structural composition, annual succession and responses to environmental factors of phytoplankton functional groups in the river courses in the urban area of Suzhou, a bimonthly survey and its analysis were conducted in 2018. A total of 209 phytoplankton species were identified from 85 genera and 7 phyla throughout the year, 29 phytoplankton functional groups were markerd out, among which 19 (B, C, D, G, H1, J, Lo, M, MP, P, S1, S2, T, TC, W1, X1, X2, Y and Z) were the dominant functional groups in this area. The annual succession of phytoplankton functional groups was characterized as follows:B+C+D+H1→W1+H1→P+G+H1→M+S1+H1. H1 was found to be dominant throughout the year. The RDA analysis showed that water temperature (WT), total nitrogen content (TN), total phosphorus content (TP) and electrical conductivity (Ec) were identified as the main factors affecting the changes in phytoplankton functional groups in the urban river courses of Suzhou City.