Endophytic fungi usually establish a symbiotic relationship with the host plant and affect its growth. In order to evaluate the impact of endophytic fungi on the Chinese herbal medicinal plant Thunb., three endophytes isolated from the rhizomes of , namely (IL), unidentified fungal sp. (UF), and (PC), were co-cultured individually with in sterile soil for 60 days. Analysis of the results showed that the endophytes stimulated the host plant in different ways: IL increased the growth of rhizomes and the accumulation of most of the phenolics and volatiles, UF promoted the accumulation of the medicinal compounds afzelin, decanal, 2-undecanone, and borneol without influencing host plant growth, and PC increased the fresh weight, total leaf area and height of the plants, as well as the growth of the rhizomes, but had only a small effect on the concentration of major secondary metabolites. Our results proved that the endophytic fungi had potential practical value in terms of the production of Chinese herbal medicines, having the ability to improve the yield and accumulation of medicinal metabolites.