Abstract In recent years, the use of biological methods to control water bloom has become an ecological approach. In this research, the effect of total flavonoids extracted by ethanol in Cirsium japonicum DC seeds on Microcystis aeruginosa cell density and morphological changes was assessed via six treatments (0, 10, 20, 30, 40, and 50 mg/L). Chlorophyll a, carotenoid, phycocyanin (PC), and allophycocyanin (APC) content were analyzed. Also, adversity indicators variance including malondialdehyde (MDA), O2−., and antioxidant isozyme activity of superoxide dismutase (SOD) and ascorbate oxidase (APX) were revealed. The results showed M. aeruginosa density was significantly influenced by C. japonicum DC total flavonoids in a negative dose-response. After 9 days of treatment, density decreased by 58.8%, and algal cells shrank severely under treatment of 50 mg/L total flavonoids. In addition, the chlorophyll a, carotenoid and PC content displayed a decreasing trend compared to the control, meanwhile contents of MDA, APC (except 50 mg/L treatment), activity of O2−., SOD and APX increased. This study shows the total flavonoids of C. japonicum DC has higher biological activities and can interfere with growth of M. aeruginosa. It was concluded that C. japonicum DC may be useful to control harmful water bloom.