Abstract: In this study, Aconitum carmichaelii Debx. and rhizosphere soil from different areas were studied. The changes of endophytic microorganisms, soil microorganisms, alkaloid content and soil element factors of Aconitum carmichaelii were studied by illuminahiseq high-throughput sequencing technology and high performance liquid chromatography. The results showed that: the contents of benzoylneaconitine, benzoylaconitine and monoester alkaloids were positively correlated with Acinetobacter abundance, soil pH and Al³⁺ content，while negatively with Aspergillus abundance. The content of hypoaconitine was positively correlated with Bradyrhizobium abundance. However, the other two alkaloids (benzoylsubaconitine and hypaconitine) accumulations were negatively correlated with Athelia and Fusarium abundances. The results show that: changing the abundances of the key microorganism (such as Bradyrhizobium, Acinetobacter, Athelia, Fusarium and Aspergillus), and improving the Al³⁺ contents and pH in rhizosphere soil probably increase the contents of several alkaloids in Aconitum carmichaelii field management programs.