Atractylodes chinensis has always been an important medicine for disease prevention and control，but the wild resources are seriously damaged and the quality of artificial cultivation is uneven. Based on the V3+V4 region of 16S rDNA of bacteria and ITS region of fungi，Illumina NovaSeq high-throughput sequencing technology combined with bioinformatics were applied to compare the community structure of bacteria and fungi in rhizosphere soil of wild and cultivated Atractylodes chinensis. The aim of correlation analysis between rhizosphere soil microorganisms and volatile substances content was to reveal the influence of soil microecological environment on volatile substances in Atractylodes chinensis. The results showed that the dominant bacterial phyla of the two treatments were Proteobacteria，Actinomycetes and Acidobacteria. The relatively abundant bacteria in wild soil were Proteobacteria，Acidobacteria，α-Proteobacteria，NC10，Rhizobiales，Sphingomonadaceae，etc. The dominant fungal phyla in the two treatments were Ascomycota，Basidiomycota and Mortierellomycota. Fungi with relatively high abundance in wild soil included Basidiomycota，Agaricomycetes，Archaeorhizomycetales，Helotiaceae，Solicoccozyma aeria，etc. Chemoheterotrophic bacteria involved in soil carbon cycle and fungi of Penicillium were abundant in wild soil，while in cultivated soil，pathogenic fungi of Fusarium and Fusarium equiseti were abundant. The results of correlation analysis showed that most of the relatively abundant microorganisms in wild soil were significantly correlated with the contents of different types of volatile substances. This study clarified the microbial community structure of rhizosphere soil of wild and artificially cultivated Atractylodes chinensis，providing theoretical basis for functional exploration of beneficial microorganisms in rhizosphere of wild Atractylodes chinensis and biofertilide research，improving the soil microenvironment and increasing the content of medicinal ingredients of cultivated Atractylodes chinensis.