The cultivation of Fritillaria ussuriensis faces challenges due to the prevalent Fritillaria wilt disease, hindering large-scale production. To address this, we aimed to understand the disease’s characteristics and develop effective prevention measures. Microbial communities of diseased F. ussuriensis plants were analyzed, pathogenic and antagonistic strains were screened, and biocontrol feasibility was tested. We identified Botryotinia predominance in aboveground parts and variations in Mrakia, Humicola, llyonectria, and Fusarium in underground parts. The pathogens Fusarium oxysporum IFM-1 and Fusarium solani IFM-52 isolated from diseased F. ussuriensis not only caused severe Fritillaria wilt but were also pathogenic to Lilium lancifolium and Allium cepa var. aggregatum in Liliaceae. The antagonistic Bacillus tequilensis LFM-30 and Trichoderma koningiopsis IFM-47 isolated from diseased plants significantly alleviated plant wilt and showed promise in preventing wilt disease caused by Fusarium in Liliaceae plants. Our study highlights distinct microbial differences between healthy and diseased F. ussuriensis and underscores the pathogenicity of Fusarium. Using T. koningiopsis and B. tequilensis either singly or in combination could offer effective biocontrol against F. solani and F. oxysporum, benefiting F. ussuriensis and related Liliaceae plants.