A new method for algal community restructuring is proposed, where harmful algae growth is inhibited through the addition of remedial nano-agent, while probiotic algae growth is promoted or only affected indistinctively. In this paper, the inhibiting effects of five different nanomaterials on Microcystis aeruginosa (M. aeruginosa) and Cyclotella sp. were studied, and the optimal nanomaterial was served as algae-inhibition ingredient of the remedial agent. The effects of the remedial agent on algal growth and their physiological characteristics were investigated, and the restructuring of algal community in actual water samples was explored. The results indicated that the inhibition ratio of 10 mg/L nm-Cu2O/SiO2 on M. aeruginosa and Cyclotella sp. could reach 293.1% and 82.8% respectively, acting as the best candidate for algae-inhibiting ingredient. After adding the remedial nano-agent made with nm-Cu2O/SiO2, the content of chlorophyll a, protein, and polysaccharides of M. aeruginosa decreased sharply, while the physiological characteristics of Cyclotella sp. were not significantly affected. Besides, the total biomass and proportion of cyanobacteria dropped (P < 0.05), but the Bacillariophyta biomass increased significantly (P < 0.05). The uniformity index, Shannon-Wiener index, and richness index all increased significantly (P < 0.05). Meanwhile, the quality of actual water samples has been improved evidently (P < 0.001). Therefore, the prepared remedial nano-agent in this study can control the harmful algae bloom to a certain extent by restructuring the algal community in eutrophic water bodies.