The experiments of application of 0.5, 1.0, 2.0 mg/L chitosan and 25, 50 and 100 mg/L nano-carbon copper to the Microcystis aeruginosa liquid, respectively, were set to detect the concentration of algae cells and chlorophyll a mass concentration in the algae liquid, and to investigate the inhibition effects of chitosan and nano-carbon copper on Microcystis aeruginosa. In the experiments, the pH value, dissolved oxygen and copper ion residue under the conditions of 100 mg/L nano-carbon copper and 100, 500 mg/L copper sulfate were collected in the algae removal process to further verification of the inhibition effect of nano-carbon copper on Microcystis aeruginosa. The results showed that the algae inhibition effect of chitosan was not obvious, and the nano-carbon copper at 100 mg/L had obvious antibacterial effect, and the concentration of algal cells added to the 100 mg/L nano-carbon copper group was significantly lower than those of other groups at 144, 360 and 480 h, and the concentration of algal cells decreased significantly over the increase of culture time at 72-480 h. At 48-240 h, the mass concentration of chlorophyll a and the residual amount of copper ion in algal liquid with the addition of 100 mg/L nano-carbon copper group were significantly lower than those of the 100 and 500 mg/L copper sulfate groups, while small change in the pH value. Collectedly, this reveal that 100 mg/L nano-carbon copper can effectively inhibit Microcystis aeruginosa, the residual amount of copper ions and the pH change in water bodies are small, and it can be widely used in aquaculture.