In China, Polygonatum cyrtonema Hua (Huangjing) is known for its medicinal and edible properties. Multiple environmental factors can shape plant-microbiome interactions. The cultivated sample sites were enriched characteristic fungi by Clonostachys divergens and Archaeorhizomycetes spp. whereas wild sample sites were enriched particular by Geminibasidium spp. and Bifiguratus spp. The number of observed species was lower in cultivated soil samples compared with wild ones by alpha diversity analysis. Functional annotation showed that the xylanolysis metabolism pathway was more abundant in rhizosphere microorganisms of cultivated P. cyrtonema Hua. The co-occurrence network showed positively interacted between Mucoromycota and Rozellomycota in the cultivated rhizosphere soil. Moreover, this result indicated that biomass of cultivated plant was significantly greater than that of the wild samples, and the polysaccharide content of the cultivated rhizomes was higher. In this study, we may predict basic and potential microbes that beneficial for the P. cyrtonema Hua rhizosphere improve the productivity and quality.