Qingcaosha Reservoir, a reservoir located at the Yangtze River Estuary, is the largest water source of Shanghai. As a semi natural semi artificial reservoir, its ecosystem is affected by source water, but also influence by its own unique temperament. Rotifers are one of the most effective organism group as monitors for water quality. It can well reflect the current status of water in reservoirs, such as the eutrophication timely and provide the biological reference for reservoir management. The community structure of rotifer was investigated from 2014 to 2015 according to the characteristics of rotifers horizontal distribution and temporal distribution. We took the data on the species composition, dominant species, quantitative distribution and community characteristics of rotifer and used cluster analysis to analyze the diversity index of Rotifer Community Structure. Redundancy analysis was used to illustrate the relationship between rotifers and environmental factors. Total of 32 species of rotifers were identified in two year period. Of which 20 species were recorded in the year 2014 with 7 dominant species; twenty six species with 2 dominant species were collected in 2015 (Table 2, 3, Fig. 5). The Polyarthra trigla was the only one species dominantly in the two years. Among those 8 species belonged to oligo group with a lower density (156.37 ± 119.48 ind/L) in 2014 than that in 2015 (237.12 ± 252.86 ind/L), respectively. The annual biomass of rotifers was higher with the number are 0.1316 ± 0.1146 mg/L in 2014 than that 0.1229 ± 0.1371 mg/L in 2015 (Fig. 2), respectively. The seasonal variation and horizontal distribution of Rotifers was showed in Fig. 3 and Fig. 4. Cluster analysis was performed based on Rotifer biomass, biomass and diversity index (Table 4, Fig. 6), the results indicated that the horizontal distribution of rotifers had a great relationship with the shape and geographical characteristics of the reservoir. Redundancy analysis (RDA) showed that water temperature, dissolved oxygen, total nitrogen, total phosphorus and density of phytoplankton were the main environmental factors which influenced the density of Phytoplankton in the reservoir (Table 5, Fig. 7).