To understand the characteristics of phytoplankton community structure in Xin’anjiang River Basin (Anhui section) and its tributaries, water samples were collected from 15 stations in both main stream and tributaries in flood season of 2016 and 2017. The functional groups were classified based on the phytoplankton community composition. The results showed that phytoplankton belonged to six phyla and fifty-five genera. Species in Bacillariophyta, Cyanophyta and Chlorophyta were in dominant groups. Higher relative abundance was found in Navicula, Gomphonema, Synedra and Cyclotella in Bacillariophyta, as well as Closterium in Chlorophyta and Euglena in Euglenophyta. There were some differences in phytoplankton community structure between different sampling stations and different years. Across all river stations, the dominant species could be classified into 27 functional groups, among which MP, D, B, J, P, Tb and W1 were distributed in all sampling stations. The MP, D, B and Tb functional groups had both higher frequency of distribution and higher relative abundance. The low or mesotrophic status of nutrients reflected by dominant phytoplankton functional groups had well correspondence with the measured water chemical parameters. Water quality in studied stations fell between type I and type III, with a few stations falling to type III. Results of redundancy analysis (RDA) showed that NH₃-N, TN, TP, and COD_Mn were the key environmental drivers determining the dominant  phytoplankton groups. Our results suggest that phytoplankton functional groups can indicate the habitat characteristics of Xin’anjiang River Basin and its tributaries. Combining phytoplankton functional groups and water chemical parameter measurement can provide sound data and basic theory for water quality monitoring and aquatic ecosystem protection in Xin’anjiang River Basin.