The cyanobacteria Microcystis flos-aquae can cause harmful algal blooms in waterbodies, which threaten the normal functioning of aquatic ecosystems and human health. Some plant extracts are considered as promising algaecides. In this study, the effects of ten plant extracts (Cinnamomum camphora, Ginkgo biloba, Firmiana platanifolia, Salix babylonica, Euphorbia humifusa, Erigeron annuus, Solidago canadensis, Alternanthera philoxeroides, Thalia dealbata and Eichhornia crassipes) against M. flos-aquae were investigated. The results showed that all ten plant extracts had a significant inhibitory effect on M. flos-aquae growth after 96 h (P < 0.01). The inhibition rates of S. babylonica, E. humifusa, S. canadensis and A. philoxeroides were over 70.00%. Furthermore, the E. humifusa extract had the best inhibitory effect on the photosynthesis of M. flos-aquae, with the effective quantum yield of photosystem II and maximal relative electron transport rate decreasing by 97.50% and 97.00%, respectively, after 96 h. Additionally, the E. humifusa extract was found to be non-toxic to non-target organisms such as Brachydanio rerio and Vallisneria spiralis within 96 h. This study contributes to the existing knowledge and data of freshwater cyanobacteria blooms, and provides insights for their control and the restoration of freshwater systems affected by cyanobacteria blooms.