Background Fritillaria taipaiensis P.Y. Li is commonly used in Chinese medicine for its cough-suppressing and expectorant properties. Due to over-excavation and ecological damage, the wild resources of F. taipaiensis have suffered serious damage. Understanding and improving the inter-root soil environment plays an important role in improving the success rate of artificial cultivation of F. taipaiensis and the quality of medicinal herbs. Methods This study employed a pot experiment to inoculate three strains of phosphorus-solubilizing fungi from the Aspergillus genus for a total of seven treatment groups, with sterile physiological saline serving as the control group (CK). The research aims to examine the impact of inoculating phosphorus-solubilizing fungi on the biomass of F. taipaiensis, alkaloid concentration in its bulbs, and characteristics of the rhizosphere soil environment. The specific inoculation treatments included: Aspergillus tubingensis (Z1); Aspergillus niger (Z2); Aspergillus fumigatus (Z3); a combination of A. tubingensis and A. niger (Z12); a combination of A. niger and A. fumigatus (Z13); a combination of A. tubingensis and A. fumigatus (Z23); and a combination of all three fungi, A. tubingensis, A. niger, and A. fumigatus (Z123). Results Inoculation with phosphorus-soluble fungi significantly increased the biomass of F. taipaiensis, and the largest increase was in the Z123 group, which was 62.85% higher than that of the CK group. Total alkaloid content increased the most (0.11%) in the Z3 group, which was an 83.87% increase compared with the CK group. The total content of monomer alkaloids in the Z3, Z13, and Z123 groups increased by 10.53%, 12.48%, and 9.61%, respectively, compared with those in the CK group, indicating that the quality of F. taipaiensis could be significantly improved after applying phosphorus-solubilizing fungi. The soil environment improved after inoculation with different phosphorus-solubilizing fungi. The Z23 and Z123 groups had the greatest effect on the rhizosphere soil bacteria and Actinomyces. Overall, the soil nutrient content of the Z13 group increased the most, and the contents of available phosphorus, available potassium, available nitrogen, total phosphorus, and organic matter increased by 47.71%, 27.36%, 26.78%, 25.13%, and 31.72%, respectively, compared with those in the CK group. Conclusion These results show that the treatment groups that included different combinations of strains were superior to the single-strain treatment groups, and the Z123 group was the best treatment group when considering bulb biomass and alkaloid and soil nutrient contents. Applying phosphorus-solubilizing fungus fertilizer is highly feasible during F. taipaiensis production in the field.