The invention discloses a Bacillus amyloliquefaciens subsp. plantarum ZFH-3 and application thereof. The classification designation of the strain is Bacillus amyloliquefaciens subsp. plantarum, and the collection number is CGMCC No.9884. The strain has obvious inhibiting actions on multiple crop pathogens, especially can effectively control postharvest diseases of fruits, is well used for biological control of contact mold of citrus fruit, olive green mould of ditrus fruit, citrus phomopsis stem end rot, sour rot of citrus, anthracnose of citrus, anthracnose of banana, spike rot of banana, gray mold of strawberry, soft rot of strawberry and other pathogen fungi, obviously lowers the possibility of postharvest diseases of fruits, prolongs the storage life and shelf life, and reduces the consumption of chemical reagents. The strain has the advantages of simple culture conditions and high reproduction speed, can easily implement industrial production, popularization and application, and has favorable development and application prospects.