Lily Fusarium wilt disease caused byFusariumspp. spreads rapidly and is highly destructive, leading to a severe reduction in yield. In this study, lily (Lilium browniivar.viridulum) bulbs were irrigated after planting with suspensions of twoBacillusstrains that effectively control lilyFusariumwilt disease to assess their effects on the rhizosphere soil properties and microbial community. A high-throughput sequencing of microorganisms in the rhizosphere soil was performed and the soil physicochemical properties were measured. The FunGuild and Tax4Fun tools were used for a functional profile prediction. The results showed thatBacillus amyloliquefaciensBF1 andB. subtilisY37 controlled lily Fusarium wilt disease with control efficacies of 58.74% and 68.93%, respectively, and effectively colonized the rhizosphere soil. BF1 and Y37 increased the bacterial diversity and richness of the rhizosphere soil and improved the physicochemical properties of the soil, thereby favoring the proliferation of beneficial microbes. The relative abundance of beneficial bacteria was increased and that of pathogenic bacteria was decreased.Bacillusabundance in the rhizosphere was positively correlated with most soil physicochemical properties, whereasFusariumabundance was negatively correlated with most physicochemical properties. Functional prediction revealed that irrigation with BF1 and Y37 significantly upregulated glycolysis/gluconeogenesis among metabolism and absorption pathways. This study provides insights into the mechanism by which twoBacillusstrains with antifungal activity, BF1 and Y37, antagonize plant pathogenic fungi and lays the foundation for their effective application as biocontrol agents.