Bacillus velezensis is a new species of Bacillus sp recently discovered. It is considered a new plant growth promoting rhizobacteria because of its ability to inhibit a variety of pathogens and promote plant growth. In this study, we isolated a novel Bacillus velezensis strain ES2-4 in orchard soil. Based on comparative analysis, including average nucleotide polymorphism (ANI), digital DNA-DNA hybridization (dDDH), and phylogenetic analysis, ES2-4 was designated as Bacillus velezensis. Genomic analysis revealed that Bacillus velezensis contains a series of genes closely related to promoting plant growth directly and indirectly. Genomic secondary metabolite analyses indicated there are 9 identified gene clusters involved in the biosynthesis of various secondary metabolites (Surfactin, Iturin, Fengycin, Bacillibactin, Bacilysin, Macrolactin, Bacillaene, Difficidin, Amylocyclicin), and five clusters encoding polyketides, lanthipeptide, terpenes, but the specific substances are unclear. In addition, Bacillus velezensis ES2-4 showed good antagonistic activity against various plant pathogens, especially Rhizoctonia solani. These findings suggest that Bacillus velezensis ES2-4 could be used as a PGPR strain to develop new biofertilizers and biocontrol agents.