Abstract: Zooplankton, an important component of aquatic ecosystem, has great value to evaluate water quality. In order to understand the zooplankton community structure and the water quality in the Shaying River Basin, 20 sampling sites were chosen to investigate the zooplankton community structure and the water quality by means of biodiversity index in the autumn of 2016. The results showed that 36 genera and 78 species of zooplankton were monitored, including 20 genera and 60 species of rotifera, 10 genera and 12 species of cladocera, 6 genera and 6 species of copepoda. The main dominant species were Polyarthra dolichoptera, Anuraeopsis fissa, Brachionus angularis, B. calyciflorus, KeratelIa valga and Bosmina sp. The highest density and biomass of zooplankton were in the upstream. The spatial variation trend of biomass and density of zooplankton were consistent from upstream to downstream with a decreasing trend. The Shannon-Wiener index ranged from 1.03 to 3.51, and the Pielou evenness index ranged from 0.26 to 0.70. A comprehensive analysis of the population and diversity index of all sampling sites showed that the pollution was more serious in the upstream, and the middle-downstream was moderate pollution. The results indicated that the water quality of the Shaying River Basin was moderate to heavy pollution.