A fungicidal composition having a synergistic effect is provided. The composition comprises active ingredients A and B. The active ingredient A is polyhexamethylene biguanide or an agriculturally acceptable salt thereof, the active ingredient B is one selected from prochloraz, epoxiconazole, benthiavalicarb-isopropyl, zoxamide, azoxystrobin, prothioconazole, difenoconazole, fenamidone, polyoxin, iprodione, acibenzolar, dithianon, pyraclostrobin, trifloxystrobin, picoxystrobin, fluazinam, thifluzamide or dimethomorph, and the weight ratio of the two ingredients is from 1:50 to 50:1. The test results show that the fungicidal composition according to the present invention has an obvious synergistic effect, and importantly, the application rate is reduced, such that the cost is lowered. The application rate of a single agent alone is effectively reduced by combining the fungicides of different mechanisms and modes of action, which is beneficial for broadening the fungicidal spectrum, retarding the resistance development of the fungi and improving the control effect.