Vernicia fordii, a tropical and subtropical oil tree, is valued for its fruit but has a slow economic return. Intercropping can alter rhizosphere soil microorganisms, either promoting or inhibiting growth, and allow multiple harvests, speeding up economic returns. In this study, Polygonati odoratum, a Chinese herbal medicine, was intercropped with V. fordii, while non-intercropped V. fordii forest and single-crop V. fordii served as comparison areas. We studied the effects of rhizome intercropping on the soil microbial community by collecting rhizosphere soil samples, conducting 16S rDNA and ITS sequencing, and performing property analysis. Intercropping significantly improved soil quality, with increases of 19.77% in soil organic matter, 36.46% in available potassium, 26.67% in alkaline hydrolysable nitrogen, and a 38.70% enhancement in sucrase activity. Additionally, this planting method has notably altered the community structure of bacteria and fungi in the soil, adjusting their composition and abundance, thus positively impacting biogeochemical processes in the environment. After the implementation of the intercropping mode, the seedling height, ground diameter, and biomass of P. odoratum (a medicinal plant) all exhibited significant increases, with respective improvements of 4.16%, 9.75%, and 28.80%. Concurrently, the contents of flavonoids and saponins also rose, with enhancements of 32.92% and 13.92% respectively. These changes strongly attest to the remarkable effect of intercropping on enhancing the quality of P. odoratum. Moreover, an in-depth predictive analysis of soil microbial ecological functions revealed that intercropping not only enhanced the nitrogen-fixing ability of soil microorganisms but also effectively reduced the risk of plant diseases. Symbiotic network analysis reveals that intercropping enhances the connectivity of soil bacterial networks, increasing their complexity through the addition of network nodes. Compared to the monocropping systems of V. fordii trees and P. odoratum, the microbial networks in intercropped systems are more tightly connected. These changes in soil microbial community structure may be closely linked to environmental factors such as organic matter content and pH value. Intercropping encourages the proliferation of specific bacterial groups (including Actinobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia) and fungal groups (such as Ascomycota and Basidiomycota). The study suggests that introducing P. odoratum alters the soil microbial community of V. fordii trees, making the rhizosphere microbial network denser and more complex. This research offers valuable insights for the management of Ford’s Fleabane plantations, with the potential to enhance agricultural strategies for greater efficiency and economic benefits.