To analyze the relationship between zooplankton community structure and food quality or food concentration, and to explore the effect of copepod trophic level change on zooplankton community, the suspended matter, free-living bacteria, phytoplankton and zooplankton samples were collected in Xidong Reservoir in Xiamen from October to December of 2014. The results showed that the community structure of zooplankton did not exhibit significant difference along the water column. The community structure of copepod between the cyanobacterial bloom stage and the non-bloom stages was similar, whereas the cladocera and rotifera during cyanobacterial bloom and non-bloom stages were significantly different. Further, our results showed that the effect of food quality on copepod was significant, the effect of food concentration on cladocera was significant, while the effect of food quality and food concentration on rotifera was significant. Food quality and food concentration were significantly correlated with water temperature, copepod biomass was significantly related with rotifera biomass, cladocera biomass was significantly correlated with food concentration. In order to explore the relationship between copepod and food quality, the dominant species (Phyllodiaptomus tunguidus) was selected to analyze the stoichiometric characteristics. The results showed that the phosphorus content of P. tunguidus body was significantly and positively correlated with the average concentration of total phosphorus in water column and water temperature. The trophic level of P. tunguidus varied from 1.28 to 2.84 during the investigation period, and the trophic level increased significantly with the decrease of water temperature. Our results showed that the high quality of food in non-bloom stage was one of the reasons for the high abundance of P. tunguidus. In non-bloom stage, the joint effects of water temperature decrease and population reproduction led to decrease in the phosphorus content of P. tunguidus, and increase in the trophic level. These results provide the fundamental data for revealing the dynamic processes and mechanism of zooplankton community in eutrophic inland waters.