Phytoplankton is a key primary producer in inland water ecosystem because its community structure can indicate the water quality. To understand the phytoplankton community structure and the water quality state in Huaihe River Basin, 217 sites were set and the phytoplankton samples were collected in the basin in May 2013. The 244 taxa of phytoplankton (species and variety species) belonging to 104 genera 8 phyla were identified, of which the most abundant phyla is Chlorophyta, followed by Bacillariophyta. The average phytoplankton biomass was 3.93 mg/L, ranging from 0.04 to 83.62 mg/L, while Dinophyta, Bacillariophyta and Cryptophyta were major groups upon the biomass. The richness and biomass of phytoplankton was low in the small streams and the pathway to the sea, but high in the middle of the river. The main dominant species were Cryptomonas erosa, Chroomonas acuta, Cyclotella meneghiniana and Ceratium hirundinella, whose relative biomass were higher than 5%. The phytoplankton diversity index was low and most sites were in a medium-heavy pollution state.