To clarify the characteristics of rotifer community structure and distribution，and environmental affecting factors in the mainstream of Yangtze River，the habitat space of 27 river segments from the source to the lower reaches of the Yangtze River mainstream were divided into four regions based on physical and chemical parameters of water quality.The community structure and distribution of rotifers in the high mountain area，canyon area，plain area and estuary area was investigated，and biological methods were employed to evaluate the water quality status of the mainstream of Yangtze River.The results showed that 85 rotifer species belonging to 37 genera were identified，containing 63 indicator species，mainly oligosmal species.There were 12 dominant species in the four research areas，and Keratella ualega and Keratella cochlearis were dominant in most water areas.The average zooplankton density and biomass were 19.66 ind./L.and 0.11 mg/L，respectively.The distribution patterns of rotifers were as follows： the density and biomass of rotifers were the highest in the canyon area，followed by the plain area，high mountain area and estuary area.The average Shannon-Wiener diversity index and Pielou evenness index were 2.62 and 0.78，respectively.Specifically，Shannon-Wiener index showed significant differences among different regions （P<0.05），and the Pielou index in each region was relatively uniform.The results of NMDs analysis suggested that the similarity of rotifers community structure between crayon and plain areas was higher than that among other areas.The RDA analysis indicated that WT，density of the phytoplankton，DO，and TP were important factors affecting the spatial distribution of rotifers in the mainstream of Yangtze River.In conclusion，the community structure of rotifers in different areas of the Yangtze River mainstream showed high spatial heterogeneity，which was jointly caused by the change of natural environment and the disturbance of human activities.