ObjectiveTo analyze the microbial diversity in the rhizosphere soil of Gastrodia elata with different yields and explore the influence of soil microorganisms on the yield of G. elata. MethodThe experiment adopted the 16S DNA and ITS high-throughput sequencing technologies to study the diversity of the bacterial and fungal community in the rhizosphere soil of G. elata with high yield （GC） and low yield （DC）. ResultProteobacteria， Firmicutes， and other unidentified Bacteria were dominant in the rhizosphere soil of G. elata. The dominant rhizosphere fungi were Ascomycota， Basidiomycota， and Mortierellomycota. There was no significant difference in microbial community abundance in the high-yield and low-yield rhizosphere soil of G. elata， but there was a significant difference in species composition. Thirty-eight microbes such as Bradyrhizobium， Schleiferilactobacillus， and Archaeorhizomyces were gathered in large numbers in the high-yield rhizosphere soil， and thirty microbes such as Fusarium， Coprinellus， and Nitrosotalea were gathered in large numbers in the low-yield rhizosphere soil. At the level of genus and species， there were six different species in the high-yield and low-yield rhizosphere soil of G. elata， among which Russula mariae， Archeaeorhizomyces， and Ilyonectria were gathered in the high-yield rhizosphere soil of G. elata， while Nitrosotalea， Coprinellus disserminatus， and Fusarium were gathered in the low-yield rhizosphere soil of G. elata. ConclusionThere are different microorganisms in the rhizosphere soil of G. elata with different yields， and it is speculated that these microorganisms are related to the yields of G. elata. The research results are expected to provide a vital theoretical basis for the follow-up study of the high yield of G. elata.