Harmful cyanobacterial blooms disrupt aquatic ecosystem processes and biological functions. However, studies focusing on the effect of cyanobacterial blooms on the functional diversity of consumers are still insufficient. To examine the interactions of cyanobacterial blooms and the diversity and composition of metazooplankton, we investigated the variation in metazooplankton and their driven variables during the cyanobacterial bloom and non-bloom periods in 2020 and 2021 in Lake Xingkai. We found that cyanobacterial blooms reduced the metazooplankton species diversity but increased their biomass, functional dispersion, and functional evenness. Generalized additive mixed model results revealed that cyanobacteria showed different effects on metazooplankton biodiversity and functional diversity during the bloom and non-bloom periods. Variance partitioning analysis indicated that cyanobacteria, physicochemical variables, and temporal variation explained 15.93% of the variation in metazooplankton during the bloom period and 20.27% during the non-bloom periods. Notably, cyanobacteria during the bloom period explained more variations in metazooplankton composition than those during the non-bloom period. Our results suggest that cyanobacterial blooms significantly impact the functional diversity and community composition of metazooplankton. Physicochemical and spatiotemporal factors may mask the effects of cyanobacteria on metazooplankton. Our findings may improve the understanding of the dynamics and responses of metazooplankton communities to environmental changes and cyanobacterial blooms disturbances and enhance our ability to assess the effectiveness of aquatic ecosystem restoration and eutrophication management.