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In this study, a novel nanomaterial Cu₂O/SiO₂ was synthesized based on nano-SiO₂, and the inhibitory effects of different concentrations of Cu₂O/SiO₂ on the growth of <i>Microcystis aeruginosa</i> (<i>M. aeruginosa</i>) were studied. At the same time, the mechanism of Cu₂O/SiO₂ inhibiting the growth of <i>M. aeruginosa</i> was discussed from the aspects of Cu²⁺ release, chlorophyll <i>a</i> destruction, oxidative damage, total protein, and the phycobiliprotein of algae cells. The results showed that low doses of Cu₂O/SiO₂ could promote the growth of <i>M. aeruginosa</i>. When the concentration of Cu₂O/SiO₂ reached 10 mg/L, it exhibited the best inhibitory effect on <i>M. aeruginosa</i>, and the relative inhibition rate reached 294% at 120 h. In terms of the algae inhibition mechanism, Cu₂O/SiO₂ will release Cu²⁺ in the solution and induce metal toxicity to algae cells. At the same time, <i>M. aeruginosa</i> might suffer oxidative damage by the free radicals, such as hydroxyl radicals released from Cu₂O/SiO₂, affecting the physiological characteristics of algae cells. Moreover, after the addition of Cu₂O/SiO₂, a decrease in the content of chlorophyll <i>a</i>, total soluble protein, and phycobiliprotein was found, which eventually led to the death of <i>M. aeruginosa</i>. Therefore, Cu₂O/SiO₂ can be used as an algaecide inhibitor for controlling harmful cyanobacteria blooms.