Zooplankton is an important part of the river food web and plays an important role in the energy flow and nutrient cycling of the river ecosystem. However, there is a lack of systematic survey of zooplankton in the main stream of the Yangtze River. During 2018–2019, fifty-one survey stations were set up in about 5000 km of the main stream of the Yangtze River. And the surveys were carried out during the fish reproductive (March to June), feeding (August to October) and wintering (November to January) seasons every year. And the zooplankton community structure and distribution in the main stream of the Yangtze River were systematically studied. The results showed: ① There were 187 species of zooplankton in the main stream of the Yangtze River, including 56 species of protozoa, 59 species of rotifers, 34 species of cladocerans and 38 species of copepods. The species of zooplankton was most abundant in the Three Gorges Reservoir. And the species of zooplankton in each river reach were as follows: 59 species in Jinsha River, 68 species in the upper reaches of the Yangtze River, 87 species in the Three Gorges Reservoir, 54 species in the middle reaches of the Yangtze River, and 56 species in the lower reaches of the Yangtze River. The species of zooplankton was the most abundant in the fish reproductive season. And the zooplankton species in the breeding season of each river reach were as follows: 45 species in Jinsha River, 56 species in the upper reaches of the Yangtze River, 47 species in the Three Gorges Reservoir, 41 species in the middle reaches of the Yangtze River, and 32 species in the lower reaches of the Yangtze River. ② The density of zooplankton in the main stream of the Yangtze River ranged from 1.12 to 644.40 ind. /L. In the middle and lower reaches of the main stream of the Yangtze River, the zooplankton densities were significantly higher than that in the upper reaches. The high value of zooplankton density generally occurred during the fish reproductive season, and the low value generally occurred during the fish feeding season. ③ The zooplankton biomass: in the main stream of the Yangtze River, the zooplankton biomass ranged from 231.78 to 45638.57×10^?5 mg/L. And the zooplankton biomass in Jinsha River, the middle and lower reaches of the Yangtze River were significantly higher than that in the upper reaches and the Three Gorges Reservoir. ④ The dominant species of zooplankton in the main stream of the Yangtze River mainly included Tintinnidium entzii, Leprotintinnus fluviatile, Arcella vulgaris, Brachionus calyciflorus, Polyarthra trigla, Mesocyclops leuckarti, Neutrodiaptomus incongruens and Nauplius. The community structure and distribution of zooplankton in the main stream of the Yangtze River showed typical lotic freshwater zooplankton characteristics. The species and numbers were poor in the river. Small animals such as rotifers and protozoa played an important role in the community. The abundance of zooplankton varied from upstream to downstream and changed with season. The research results can provide important basic data for the aquatic ecology management of the Yangtze River.