Fritillaria taipaiensis is a traditional Chinese herbal plant. Germplasm degradation usually appears during its extended years of cultivation. Aiming to explore the mechanisms of the germplasm degradation, the bacterial diversities, bio-chemical characters in the rhizospheric soils of F. taipaiensis with different cultivation years from 1 to 5 were analyzed. The result showed the Chao1 and the ACE indices of the bacterial community had no significant difference among samples while the Shannon and Simpson indices declined with the cuntivation year; the dominant bacteria phylum was Proteobacteria, the remaining phyla were Chloroflexi, Nitrospirae, Planctomycetes, Actinobacteria, Gemmatimonadetes, Firmicutes, Verrucomicrobia, Bacteroidetes, and Acidobacteria; the relative abundances of the dominant bacterial genera changed obviously among samples; the bacterial community structures in the rhizospheric soils with cultivation years of 2 and 4 were significantly different from that in other samples; the content of organic matter, available N, available P, available K and the activities of urease, alkaline phosphatase in samples decreased with the cultivation years; the soil pH increased with the cultivation years to unsuitable for F. taipaiensis growth; the distance-based redundancy analysis showed the pH, organic matter content, available phosphorus content and urease activity were the primary factors in determining bacterial community composition, the intra group beta diversity of the rhizospheric bacteria increased after a initial decline with the cultivation year. These results indicated long term continuous cropping changed the bacterial community structure, fertility condition and soil enzyme activities in the F. taipaiensis rhizosphere soils, which could badly affect its growth.