Bacillus amyloliquefaciens (BA) is one of the most promising bacteria for plant growth promotion (PGP) without harmful side effects. As an excellent agent for biofertilizer and biocontrol in agriculture, the PGP mechanisms of BA have been studied extensively. However, these studies have been rarely summarized, although it could hinder a better understanding of BA strains’ potential mechanisms and application in agriculture and other fields. Hence, we reviewed in this work the PGP mechanisms of BA and the current limits of BA application in agriculture. First, BA can improve soil nutrient availability, including improving nitrogen supply, solubilizing phosphate and potassium, and producing siderophores. Second, BA can change the soil microbial community and improve the availability of minerals and plant growth conditions. Third, BA can secrete hormones and volatile organic compounds (VOCs) associated with plant cell growth and root development and further improve nutrient uptake by plants. Fourth, BA can enhance plant resistance against biotic stresses from soil pathogens through competition of niches and nutrients, producing substances such as cyclic lipopeptides, polyketides, and VOCs to antagonize pathogens directly, and induction of system resistance of the plants. Similarly, inoculation with BA can promote plant growth by inducing systematic tolerance to abiotic stresses by leading to genetic, chemical, and physical changes in the host plant. We further suggested that, in future studies, more attention should be paid to nutrient uptake mechanisms of plants with advanced techniques in different soil conditions and fields.