Phytoplankton community structure in three regions of Gehu Lake was investigated and analyzed from July in 2013 to June in 2014.The three regions include inside and outside of bio-manipulation pen and demonstration project area. A total of 158 phytoplankton species, belonging to 7 phyla and 80 genera, were identified.There were 11 dominant species of phytoplankton in inside of bio-manipulation pen, 9 dominant species of phytoplankton in outside of bio-manipulation pen and 5 dominant species of phytoplankton in demonstration project area. The main dominant species inside and outside of bio-manipulation pen throughout the year was: Microcystis incerta, and in demonstration project area was Melosira granulate var. angustissima.The order of standing crop is: outside of bio-manipulation pen > inside of bio-manipulation pen>demonstration project area. LSD from multiple comparison showed that density of phytoplankton had significant difference between inside and outside of bio-manipulation pen(P<0.05).Extremely significant difference was found between inside of bio-manipulation pen and demonstration project area(P<0.01), between outside of bio-manipulation pen and demonstration project area(P<0.01). Biomass of phytoplankton had extremely significant differences between inside of bio-manipulation pen and demonstration project area(P<0.01), between outside of bio-manipulation pen and demonstration project area(P<0.01).There was no significant difference between inside and outside of bio-manipulation pen. RDA and Pearson showed that water temperature(WT), Chl.a and COD_Mn were the main environmental variables affecting the community structure of phytoplankton.