To study the metazoan zooplankton community structure and water quality, we investigated the amount of metazoan zooplankton and the water quality in Gaoyou Lake from January to December 2022. Furthermore, we also evaluated the multi-index and nutritional status of Gaoyou Lake using the comprehensive nutritional status index of water quality, dominant population composition of the metazoan zooplankton, B/T index, and Shannon–Weaver diversity index based on the situation of each ecological and functional zone. The results indicated that the metazoan zooplankton of Gaoyou Lake included 21 families, 31 genera, and 63 species. The rotifers had 8 families, 16 genera, and 34 species, accounting for 53.9% of all species. The cladocerans had 6 families, 7 genera, and 16 species, which accounted for 25.4% of all species. The copepods had 7 families, 8 genera, and 13 species, that accounted for 20.7% of all species. The density and species of small metazoan zooplankton (rotifers) had a higher proportion than large metazoan zooplankton (crustaceans). The average annual metazoan zooplankton density was 1595.7 ind./L, the average annual biomass was 4.31 mg/L, the average annual total nitrogen (TN) was 1.101 mg/L, and the average annual total phosphorus (TP) was 0.082 mg/L. The TN and TP of the Gaoyou Lake were over the standard. The comprehensive nutritional status indices of the water quality in the entire lake and the ecological and functional areas were consistent with the metazoan zooplankton evaluation results, which determined that Gaoyou Lake showed mild eutrophication.