Longya Lily (Lilium brownii var. viridulum) bulb rot, a devastating soil-borne disease caused by Fusarium oxysporum f. sp. lilii (Fol L1-1), severely compromises yield and quality of this economically significant crop. In this study, strain R12 was isolated from the rhizosphere soil of asymptomatic Longya lily plants and identified as Bacillus velezensis. The strain significantly disrupted the spore germination and hyphal morphology of Fol L1-1. In pot experiments, R12 not only effectively suppressed disease development but also promoted plant growth, a trait potentially linked to its indole-3-acetic acid (IAA) production capacity. Genomic analysis revealed a 4,015,523 bp circular chromosome (46.42% GC content) harboring gene clusters for the synthesis of diverse secondary metabolites, including surfactin, fengycin, difficidin, and bacillibactin. These findings highlight the potential of B. velezensis R12 as a biocontrol agent and provide insights into its mechanisms for suppressing phytopathogens and promoting plant growth.