Abstract: Bacillus velezensis, a recently identified species within the Bacillus genus, has emerged as a versatile biocontrol agent in sustainable agriculture. There are also multifaceted antimicrobial activities, plant growth-promoting traits, and environmental resilience. This review aims to systematically delineate the organism’s taxonomic evolution, mechanistic roles in the preharvest and postharvest disease management, cutting-edge genetic engineering strategies, and future prospects. 1) Initially isolated from the Vélez River in Spain in 2005, B. velezensis was reclassified as a distinct species in 2016. Polyphasic taxonomy was also integrated with 16S rRNA phylogeny, DNA-DNA hybridization, and pan-genomic analysis. Representative strains, such as FZB42, have specialized biosynthetic gene clusters responsible for lipopeptides like surfactin and iturin, polyketides, and siderophores. Comparative genomics revealed that there were unique adaptations of B. velezensis. A tripartite strategy was employed against phytopathogens. First came the direct antagonism. Some B. velezensis was used to secrete the chitinases, cellulases, or β-glucanases, in order to degrade the fungal cell walls. Surfactin and lipopeptides, like fengycin A, disrupted the bacterial membranes. And the volatile organic compounds like 2,3-butanedione also inhibited the bacterial growth, and then came the induced systemic resistance. The organism was used to secrete the salicylic acid, in order to promote the signal transmission in plants, and lipopeptides to trigger the defence mechanism of plants. Also, B. velezensis induced the plants to secrete an enzyme in order to enhance their defence. In watermelon, the strain WB upregulated the phenylalanine ammonia-lyase activity, thus triggering callose deposition for the lower Fusarium wilt incidence. Last was growth promotion. The NKG-2 strain produced the indole-3-acetic acid to promote plant growth. Meanwhile, B. velezensis was used to enhance iron, nitrogen, and mineral assimilation in plants. There were special advantages of B. velezensis over the rest biocontrol agents. Compared with B. amyloliquefaciens, B. velezensis shared a stronger environmental adaptability. Compared with Pseudomonas fluorescens, the antibacterial substances from B. velezensis were more stable in producing the iron carriers in an iron-rich environment. Compared with the chemical pesticides, B. velezensis promoted the proliferation of beneficial bacteria by secreting iron carriers to alleviate the soil salinization after colonization, thereby increasing the soil microbial index without harming aquatic organisms. 2) Next was to evaluate the genetic modification system of B. velezensis. Firstly, the current bioinformatics analysis of multiple strains was introduced on the gene clusters to synthesize lipopeptides and ketones. And the transcriptomic analysis of some expressions was proposed as well. Then, the DNA elements were introduced to be identified by B. velezensis at present, including promoters, manipulators, and CRISPR Cas elements. Meanwhile, the electrical transformation of B. velezensis was clarified to optimize the transformation efficiency. 3) Finally, the gene editing was applied to B. velezensis, namely, homologous recombination, CRISPR-Cas9, and RNA interference. Until 2024, homologous recombination was the most widely used genetic modification for B. velezensis. But it was limited by its low accuracy. Bioinformatics analysis and synthetic biology were integrated to revolutionize the biocontrol paradigms. Current technical limitations have accelerated its transition from laboratory research to scalable agricultural solutions, aligning with the global demands for sustainable food production.