The invention discloses a sterilization composition containing hexamethylene flusulfamide and penthiopyrad and an application of the sterilization composition. The sterilization composition takes the hexamethylene flusulfamide and the penthiopyrad as main effective components, and the mass ratio of the hexamethylene flusulfamide to the penthiopyrad ranges from 1:50 to 70:1. The sterilization composition can be applied to prevention and treatment of cereal, fruit tree and vegetable diseases, has high synergetic effects, overcomes and delays drug resistance of pathogenic bacteria and is high in sterilization speed and long in lasting period, application cost is reduced, and prevention and treatment effects are obviously superior to those of single dosage. The sterilization composition can be used for preventing and treating fungal diseases of crops, and particularly can be used for preventing and treating the fungal diseases such as scab, sclerotium diseases, sheath blight, powdery mildew, rust diseases, gray mold and downy mildew. The effects of the sterilization composition are better than those of single dosage.