Fritillaria taipaiensis is a valuable traditional Chinese medicinal plant affected by germplasm degradation during cultivation. To find a suitable solution for this problem, F. taipaiensis was inoculated with exogenous arbuscular mycorrhiza (AM) fungi, potassium-solubilizing bacteria, and phosphorus-solubilizing bacteria in pot experiments. The effects of inoculation on the AM colonization, photosynthetic pigment, and superoxide dismutase contents, rhizospheric enzyme activities, alkaloid, and nucleotide content of F. taipaiensis were studied. The results showed that the inoculation increased mycorrhizal infection intensity of F. taipaiensis. Compared to the control group, the photosynthetic pigment contents in the leaf of the inoculation groups were increased; the content of soluble protein, the activities of the superoxide dismutase, catalase, and peroxidase in leaves were all significantly increased, and the content of malondialdehyde was decreased. The microbial inoculum also increased the content of active ingredients in F. taipaiensis bulbs and increased the enzyme activities, total microorganism number, bacteria/fungi, and actinomycetes/fungi ratios in the rhizosphere. To sum up, microbial fertilizer can significantly improve the rhizospheric environment and medicinal quality of F. taipaiensis. This research provides a theoretical basis and experimental evidence for the sustainable development of an F. taipaiensis industry.