The invention discloses application of bacillus amyloliquefaciens in preventing and controlling fungal disease of plants. The application has the advantages that found by study, the bacillus amyloliquefaciens, especially bacillus amyloliquefaciens BSY3 separated and screened from African marigold by an inventor, has obvious antagonistic function on phellinus noxius, pyricularia cannaecola hashioka, sclerotinia sclerotiorum, colletotrichum sp., pestalotiopsissp, fusarium oxysporum f.sp.cubense and the like, and has obvious biological control function and potential application value on preventing and controlling of the fungi diseases due to pathogenic bacteria; the bacillus amyloliquefaciens comes from endophytic bacteria in plants, so that compared with the traditional chemical agent preventing and control method, the safer biological control effect on the fungi diseases is realized; because the bacillus amyloliquefaciens stays in the plant for a long time, the survival relationship with harmonious coexistence and stable development is established with the plant; compared with the chemical agent, the biocontrol function can be more effectively and stably realized.