Zooplankton community structure is a key indicator of lake ecosystem health. Understanding its spatiotemporal dynamics and environmental drivers is of great significance for ecological conservation and water environment management. The Huayanghe Lakes, located in the middle and lower reaches of the Yangtze River, is a typical sluice-controlled river-connected lake group and an important regional drinking water source. Clarifying the spatiotemporal variations and driving mechanisms of metazoan zooplankton community structure in this lake group is therefore important for lake ecological protection, water quality improvement, and drinking water source management. In this study, systematic investigations of metazoan zooplankton community structure and physicochemical water parameters were conducted in the Huayanghe Lakes in April 2023 (spring), July 2023 (summer), October 2023 (autumn), and January 2024 (winter). Redundancy analysis (RDA) and variation partitioning analysis (VPA) were used to explore the main driving factors of community structure. During the survey period, a total of 67 metazoan zooplankton species belonging to 50 genera were identified, including 37 Rotifer species from 23 genera, 15 Cladoceran species from 14 genera, and 15 Copepod species from 13 genera. The abundance and biomass ranged from 21 to 956 ind./L and 2.83 to 17.09 mg/L, respectively. Temporally, metazoan zooplankton community structure showed obvious seasonal differences. Abundance was highest in autumn, biomass was highest in spring, and both abundance and biomass were lowest in summer. The number of dominant species, Shannon-Wiener diversity index, and Pielou evenness index were higher in autumn and winter than in spring and summer, whereas the Margalef richness index reached its maximum in summer. Spatially, metazoan zooplankton abundance and biomass followed the pattern: Longgan Lake > Huangda Lake > Bo Lake, while Margalef richness, Shannon–Wiener diversity, and Pielou’s evenness indices showed the opposite pattern: Bo Lake > Huangda Lake > Longgan Lake. Environmental driving analysis indicated that the key factors influencing metazoan zooplankton community structure varied across temporal and spatial scales. Temporally, zooplankton communities were positively correlated with suspended solids (SS) and ammonium nitrogen (NH4+-N) in spring, dissolved total phosphorus (DTP) and phosphate (PO?3?–P) in summer, phosphate (PO?3?–P) and permanganate index (CODMn) in autumn, and total phosphorus (TP) and dissolved oxygen (DO) in winter. Spatially, SS, PO?3?–P, and water transparency (SD) were the primary factors driving the community structure in Longgan Lake, Huangda Lake, and Bo Lake, respectively. The VPA results showed that water environmental factors and sluice-controlled hydrological factors jointly explained 54.7% of the variation in metazoan zooplankton community structure, with independent explanation rates of 28.1% for water environmental factors and 17.4% for hydrological factors, and a shared explanation rate of 9.2%. These results indicate that sluice-controlled water level processes play an important role in shaping community structure by affecting water exchange, suspended sediment transport, and nutrient distribution. Seasonally, the Huayanghe Lakes were in an oligotrophic–mesotrophic and oligosaprobic condition in summer, while eutrophic and α-mesosaprobic conditions were observed in spring, autumn, and winter. Spatially, Bo Lake was classified as oligotrophic–mesotrophic and oligosaprobic, Huangda Lake as mesotrophic and α-mesosaprobic, and Longgan Lake as eutrophic and β-mesosaprobic. Overall, the zooplankton community structure in the Huayanghe Lakes exhibited significant spatiotemporal heterogeneity, driven by multiple environmental factors, including nutrients, suspended solids, and dissolved oxygen. These findings provide a scientific basis for ecological protection, eutrophication control, and drinking water source management in the Huayanghe Lakes.