Amomum villosum Lour. is a perennial herb of the Zingiberaceae family, which is widely distributed in Xishuangbanna, Yunnan Province in Southwest China. Large amounts of volatile components contained in this plant enter the surrounding atmosphere and soil through volatilization, foliar leaching, root exudation, and residue decomposition. However, the ecological role of these compounds is currently unclear. The aim of this study was to compare the differences in the composition of volatile oils from stems, leaves, and young fruits of A. villosum, identify chemicals that had allelopathic effects, and explore the effects of the oil on the diversity and composition of soil microbiomes. Volatile oils were obtained by steam distillation and characterized by gas chromatography–mass spectrometry, and then were tested for allelopathic activity using seedlings of Lactuca sativa L. and Lolium perenne L. as test species. The results showed that the oils from stems and leaves were rich in monoterpene hydrocarbons, unlike the oxygenated monoterpenes which dominated oils from young fruits. Leaves > stems > young fruits: this was the order of the allelopathic effects of volatile oils from various A. villosum organs. Among the four main chemical components in the oils, only α-pinene, which is abundant in leaves, had a stronger allelopathic action than the crude oils, implying that it might be a potential allelochemical. Experiments on soil microorganisms indicated that 3.0 mg/mL oil had the greatest effect on the structure of the soil fungal community. It can be concluded that A. villosum is capable of releasing allelochemicals which affect the growth of other plant species and the diversity and community structure of soil microorganisms.