Harmful cyanobacterial blooms in eutrophic water bodies have frequently occurred worldwide and become a major environmental concern. Therefore, it is imperative to develop a stable and efficient algaecide to solve this issue. In this study, our purpose was to investigate the efficacy and mechanism of a newly developed Cu2+ doped Fe3O4@Biochar magnetic composite (Cu-Mag-BC) in in-situ inactivation of Microcystis aeruginosa (M. aeruginosa). We successfully synthesized the Cu-Mag-BC by coating Cu2+ onto Fe3O4@Biochar. Cu-Mag-BC exhibited super-paramagnetic behavior and was uniformly impregnated by Cu2+. Cu-Mag-BC (5 mg/L), rapidly inactivated chlorophyll-a (Chl-a) in M. aeruginosa with low Fe and Cu leaching, during which time the OD(26)4 value and malondialdehyde (MDA) content increased, while the activities of superoxide dismutase (SOD) and catalase (CAT) first increased and then decreased, due to oxidative stress induced by over-generated reactive oxygen species (ROS). Quantitative results showed that center dot O-2(-) and center dot OH were the main ROS species produced from Cu-Mag-BC. Inactivation efficiency was maintained at approximately 80 % after three consecutive runs and total Chl-a removal efficiency reached 2.84 g/g, indicating good reusability and stability. A possible inactivation mechanism is proposed; amino groups and adipose chain were the primary oxidation sites. Thus, Cu-Mag-BC shows potential as a candidate for simultaneously inactivating harmful cyanobacteria and preventing secondary pollution.