From July 2013 to June 2014, in late every month comparative experiment was carried out to study the community structure of rotifer in three regions of Lake Gehu. The three regions include dredging area, inside and outside of bio-manipulation area. Using freshwater plankton survey method to study the relationship between species composition, dominance, standing crop, species diversity of rotifers and water quality parameters. A total of 51 species of rotifer were collected and identified, belonging to 14 families and 22 genera. Dominant species throughout the year were: Brachionus angularis, Polyarthra trigla, Keratella valga, Polyarthra dolichoptera and Filinia longiseta. Canonical correspondence analysis (CCA) showed that water temperature (T), dissolved oxygen (DO), permanganate index (COD_Mn), total nitrogen(TN) and total phosphorus(TP) were the main environmental variables affecting the community structure of rotifer. Multiple comparison showed that density of rotifer inside of bio-manipulation pen was significantly lower than that outside of bio-manipulation pen(P<0.05). Inside and outside of bio-manipulation pen extremely significantly lower than dredging area(P<0.01). The annual average density of rotifers: inside of bio-manipulation area [(428±96)ind/L]< outside of bio-manipulation area [(939±220)ind/L]< dredging area [(1216±330)ind/L]. The annual average biomass of rotifers: inside of bio-manipulation area [(0.364±0.100)mg/L]< outside of bio-manipulation area [(0.991±0.316)mg/L]< dredging area [(1.589±0.328)mg/L]. The experiment showed that the silver and bighead carp that control algae have some good effect on eutrophication control, and dredging has certain effect on water ecological restoration.