To evaluate the plankton community structure and ecological environment in Kizil River, we investigated the plankton and water physicochemical factors in the upper, middle and lower reaches of the Kizil River during the high-water period in May and the low-water period in September of 2020. The results showed that there were 28 species and 4 phyla in the phytoplankton community, in which diatoms and green algae were dominant, with a contribution of 71.43% and 14.29%, respectively. There were 14 species and 3 phyla in zooplankton community, including seven species of rotifiers, four species of protozoans and three species of copedods. In May, the month within abundant water season, the dominant species in the Kizil River were Spirogyra communis, Arcella sp. and Rotaria tardigrada, while Spirogyra communis, Navicula oblonga, Navicula simplex, Nebela barbata and Arcella sp. were dominated in September, a month of drought season. Meanwhile, the mean density and biomass of these two plankton communities in the dry season were higher and richer than those in the wet season. The species of both communities, however, were less diversified. The values of Shannon Diversity Index of plankton in May and December were 1.83 and 2.27, indicating a status of moderate and mild pollution, respectively. The results of redundancy analysis showed that pH, transparency, and the load of ammonia were the important environmental factors affecting plankton community structure, while pH, total phosphorus, and total nitrogen were the key factors affecting zooplankton community structure. This study can provide basic data for the protection of water resources in the Kizil River.