The invention discloses Bacillus amyloliquefaciens and an application thereof. The Bacillus amyloliquefaciens is Bacillus amyloliquefaciens YB-3, and the preservation number of the Bacillus amyloliquefaciens YB-3 in China General Microbiological Culture Collection Center (CGMCC) is CGMCC No.4318. The Bacillus amyloliquefaciens YB-3 which can generate antibiotic substances which only exist in cells and are not diffused to a fermentation liquid and has the advantages of broad spectrum antibiotic range, and efficient and stable antibiotic effect can be developed into a microbe biocontrol preparation with various functions in the future.