| [Objective]In order to explore the influence of soil microenvironment on the growth and quality of F. thunbergii, [Methods]Testing the alkaloid content, the physiochemical properties of soils and the dynamic changes of rhizosphere microbiota of F. thunbergii in the seedling, flowering and harvest stages, and analyze the correlation between F. thunbergii-soil-rhizospheric microorganisms. [Results]The soil pH and organic matter content of F. thunbergii during the growth period with a trend of first decreasing and then rising, while the activity of urease and phosphatase first increased and then decreased, but the overall followed a downward trend. The soil properties of the rhizosphere all showed differences in production areas and provenances, and the differences between production areas were far greater than the differences within provenances, which indicated that the environment of the production areas would have a direct impact on the growth of F. thunbergi. Meanwhile, the diversity of rhizosphere bacterial decreased with the growth of F. thunbergii, while the diversity of fungi firstly falling and then rising. In addition, the alkaloid content of F. thunbergii is the highest in the early growth period, and its content decreases as the bulb grows. Sequencing results showed that the bacteria in the rhizosphere soil of F. thunbergii were mainly composed of Proteobacteria，Acidobacteria, Actinobacteria，Phylum Firmicutes, Bacteroidetes and Chloroflexi, while fungi were mainly composed of Ascomycota, Mucoromycotina, Chytridiomycota and Basidiomycete. Among the top 20 dominant genera, Nitrosomonadaceae-uncultured, Gemmatimonadaceae-uncultured and Methylocystaceae-uncultured have the same changing trend as the alkaloid content with the growth of F. thunbergii. Correlation analysis showed that alkaloid content was significantly related to bacterial diversity, but not significantly correlation to fungal diversity. [Conclusion]The relationship between the growth of F. thunbergii, soil factors and rhizosphere microorganisms is close and complex, and the three interact with each other. The types and diversity of bacteria are closely related to the accumulation of alkaloids from F. thunbergii, which cannot be ignored.