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 superparamagnetic 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 OD₂₆₄ 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 ·O₂⁻ and ·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.