In order to study the effects of microbial agents on the growth of Codonopsis pilosula and the microbial community structure of rhizosphere soil，three microbial agents，Bacillus subtilis，Bacillus amyloliquefaciens and Trichoderma harzianum，were applied to the C.pilosula field. The growth index and yield of C.pilosula were counted，and the physicochemical properties and enzyme activities of rhizosphere soil samples were determined. The changes of microbial community structure were analyzed by high-throughput sequencing technology. The results showed that all three microbial agents promoted the growth and yield of C.pilosula to varying degrees，and improved the physicochemical indicators and enzyme activity of rhizosphere soil. After treated with Bacillus subtilis，the root length，root thickness，fresh weight of underground parts，dry weight of underground parts and equivalent yield indicators of C.pilosula were increased by 22.51%，28.67%，27.68%，29.99% and 20.15%，respectively，compared to the control. The organic matter，available potassium，alkali hydrolyzable nitrogen，available phosphorus，total nitrogen and total phosphorus content were increased by 28.00%，33.97%，33.85%，71.23%，17.60% and 53.23%，respectively，which were better than the other two bacterial agents. The treatment with Bacillus amyloliquefaciens showed the best effect on enzyme activity，with urease，alkaline phosphatase，catalase and sucrase activities increasing by 51.32%，114.04%，7.70% and 23.96%，respectively，compared to the control. The analysis of microbial community structure showed that microbial agents increased the relative abundance of dominant bacterial groups such as Proteobacteria，Bacteroidetes and Actinobacteria，as well as beneficial bacteria such as Sphingomonas and Gemmatimonas in the rhizosphere soil，while reducing the relative abundance of dominant fungal communities such as Actinobacteria，Sphingomonas and Fusarium in the rhizosphere soil fungal community. Relevant analysis showed that the main dominant communities of bacteria such as Proteobacteria and Bacteroidetes are significantly positively correlated with physicochemical properties and enzyme activity indicators(P<0.01)，while the main dominant communities of fungi were significantly negatively correlated with physicochemical indicators such as available potassium，available nitrogen，available phosphorus and organic matter(P<0.01). In summary，all three bacterial agents could be promoted and used in the field of C.pilosula，with Bacillus subtilis showing better efficacy. The results of this study provided a theoretical basis for the organic cultivation and sustainable development of C.pilosula.