Fritillaria taipaiensis is a valuable traditional Chinese medicinal plant that has experienced continuous decline over its cropping area. The present study aims to explore the reasons for the quality and growth decline. The fungal diversities and biochemical factors in its rhizospheric soils with cultivation duration from 1 up to 5 years were analyzed and compared. The results showed that rhizospheric fungi of F. taipaiensis belong to six phyla, including Neocallimastigomycota, Glomeromycota, Basidiomycota, Chytridiomycota, Zygomycota and Ascomycota. Thirteen genera (Pseudogymnoascus, Fusarium, Mortierella, Colletotrichum, Laetinaevia, Gibberella, Synchytrium, Lysurus, Trichocladium, Volutella, Monoblepharis, Aquamyces and Trichoderma) constituted the “core community” in the rhizosphere of F. taipaiensis. The dominant fungal genera varied significantly in rhizospheric soils with different cultivation years. The abundance of fungal species in the soil declined with the cultivation year generally. The pH, available P, organic matter and urease activity were the primary factors determining the fungal community composition in the rhizosphere. The content of organic matter, available N, P and K and the activities of urease and alkaline phosphatase decreased with cultivation years. The soil pH increased with cultivation years and was unsuitable for F. taipaiensis growth. These features suggested that long-term single planting altered the fungal community structure, fertility conditions and soil enzyme activities in F. taipaiensis rhizospheric soils, which could be detrimental for plant growth and quality.