In order to study the inhibitory effect of malonic acid on Microcystis aeruginosa, the changes of cell density and chlorophyll a mass concentration of Microcystis aeruginosa were determined under the action of malonic acid with different mass concentrations and different dosing methods. On this basis, the inhibition mechanism of malonic acid was analyzed through the changes of phycobiliprotein content and ultrastructure of algae cells after malonic acid was added. The results showed that the malonic acid had a strong inhibitory effect on Microcystis aeruginosa. When the mass concentration of the malonic acid was 60 mg/L, the inhibiton rate reached 87.26% on the 12th day. In the same action time, compared with batch dosing, the effect of one-time dosing of malonic acid was stronger. Under the action of malonic acid, chlorophyll a and phycocyanin decreased and photosynthesis was inhibited. Under the scanning electron microscope, it can be observed that the structure of algal cells was destroyed, and the material inside the cells leaked out, which led to the death of algal cells.