The Shanmei Reservoir is the drinking water source of Quanzhou City, Fujian Province, and it also provides water to Jinmen County, Taiwan Province. However, high pH in spring and summer in the reservoir affects water quality. Therefore, from 2020 on, we studied the response of zooplankton community structure to fish assemblage regulation by manipulating fish stocking and capture strategy and its relationship with environmental factors in the Shanmei Reservoir. Zooplankton community and environmental factors were seasonally investigated in January (winter), April (spring), July (summer), and October (autumn) for two years in 2020 and 2021. A total of 102 species were identified, belonging to 68 genera, including 41 Rotifera species (40.20%), 41 Protozoa species (40.20%), 7 Copepoda species (6.86%), and 13 Cladocera species (12.75%). The average density of zooplankton in the eight seasons was (1443.05±360.02) ind./L and the average biomass was (1.21±0.27) mg/L. The density and biomass of zooplankton in 2021 were significantly higher than those in 2020. Specifically, the density and biomass of cladocerans and copepods in 2021 were significantly higher than that in 2020. The biomass of cladocerans in the lower, middle, and upper sections of the reservoir in 2021 was significantly higher than that in the corresponding area in 2020. The dominant species of the zooplankton community were protozoa in spring and winter, and rotifers in summer and autumn. Based on the zooplankton density and biomass, the water quality of the Shanmei Reservoir was classified as a mesotrophic state in summer and an oligotrophic state in other seasons. The main environmental factors affecting the zooplankton community structure were electrical conductivity, water temperature, dissolved oxygen, nitrate-nitrogen, transparency and permanganate index. Our results indicated that manipulation of fish assemblage structure increased the density and biomass of zooplankton in the Shanmei Reservoir. Based on this, we proposed measures to change the zooplankton community structure by manipulating fish assemblage structure for improving water quality, which could provide scientific grounds for environment protection and efficient aquatic bio-resources utilization in lakes and reservoirs.