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The sensible use of forest resources and the sound management of forests have become increasingly important throughout the years. In keeping with the trend, a composite forestry operation model has emerged. Traditional Chinese culture and forest management are particularly intertwined in China. Thus, use of the forest–medicine compound management model is recommended. The majority of research on the management of forest–medicine compounds has focused on how to grow more effective medicinal plants, ignoring the effects of the chemicals used on the soil environment, particularly the soil micro-environment. A forest–medicine system was established in South China to investigate the impacts of planting Aspidistra elatior on the variety of rhizospheric microorganisms and their ability to use carbon sources. In the plots with or without A. elatior, three dominant plants (Castanopsis hystrix, Psychotria rubra, and Ficus hirta) grew soil rhizosphere microbes, which were analyzed using Biolog EcoPlates. The study found that planting medicinal plants in the understory improved the soil’s nutritional content, increased the inter-root microbial communities of other medicinal plants, and enhanced the microbes’ ability to use soil carbon sources. The forest–medicine complex model, which rationalizes the use of forest clearings and generates economic and ecological benefits, can significantly increase the quantity of dominant microorganisms and enhance the enrichment of other species, resulting in a positive impact on the soil environment. These findings suggest that the forest–medicine compound management model can improve the use of soil carbon sources throughout the forest system. Full article