The antibacterial activity and mechanism of COS against Aspergillus niger, Aspergillus ochraceus and Aspergillus variegatus were studied. The inhibitory activity of COS was revealed by minimum inhibitory concentration (MIC), mycelial growth inhibition rate and spore germination inhibition rate. The test data showed that COS could significantly inhibit the growth of spoilage fungi, and its MIC for the tested fungi ranged from 15.6 to 31.2 mg/mL. After COS treatment, the cell membrane of spoilage fungi produced concave folds, the cell permeability increased, and a large number of cell components leaked, indicating that the cell membrane was damaged; COS also dose-dependently reduced the production of chitin, enhanced chitinase activity, and made a large amount of soluble protein extravasate. In general, COS can inhibit the activity of spoilage fungi, mainly through the effects of cell wall, cell membrane and cell metabolism. It can be widely used in food industry as an effective antifungal natural compound.