The invention discloses a bactericidal composition containing pyraclostrobin and prothioconazole and application thereof. The bactericidal composition uses the pyraclostrobin and prothioconazole as main effective components, wherein the weight ratio of the pyraclostrobin to the prothioconazole is (1-70):(1-50). The bactericidal composition can be used for preventing and treating diseases on cereals, melons and fruits, or vegetable crops, has higher synergic effect, overcomes and postpones the drug resistance of pathogenic bacteria, has the advantages of high bactericidal speed and long duration time, lowers the use cost, and has obviously better preventing and treating effects than a single agent. The bactericidal composition can be used for preventing and treating fungus diseases on the crops, especially can be used for preventing and treating leaf blight, rust disease, powdery mildew, downy mildew, epidemic disease, anthracnose, scab, brown spot, seedling blight, gray mold, banana freckle, penicilliosis and other fungus diseases, and has better effect than a single agent.