Bacillus amyloliquefaciens have beneficial biological characteristics and can produce many kinds of antimicrobial active substances. They own important physiological and biochemical functions, such as biofilm formation and colonization in plants, promoting plant growth and induction of salt tolerance in plants, etc. In this review, we summarized the molecular mechanisms study using multi-omics analysis progress of Bacillus amyloliquefaciens in studying antimicrobial activity, colonization, growth promotion and salt tolerance induction of plants, with the aim of better application of Bacillus amyloliquefaciens.