The zooplankton community structures at 11 sampling sites in the mainstream of Huaihe River were investigated in March, June, September and December of 2011. A total of 206 species belonging to 79 genera were identified. Protozoa has 69 species (33.5% of the total) of 27 genera; Rotifer has 104 species (50.5%) of 35 genera; Cladocera has 27 species (13.1%) of 12 genera, and Copepoda has 6 species (2.9%) of 5 genera. Consequently, the number of species showed a steady decreasing trend from the upper reaches to the lower reaches. The density and biomass of zooplankton were 3527447 ind./L and 2452 mg/L, respectively. The abundance of protozoa and rotifer were on predominance, and the biomass of rotifer was on predominance. The middle reaches had the highest abundance and biomass of zooplankton. The Shannon-Wiener index and Pielou evenness index of zooplankton in the upper reaches were higher than those in the middle and the lower reaches. This study showed that the water quality of the upper reaches of Huaihe River was in oligotrophic status, while the middle and lower reaches were in mesotrophic status or eutrophic status. Redundancy analysis showed that temperature, dissolved oxygen and velocity were strongly correlated with the zooplankton community structures.