Although it is well-documented that invasion of invasive plants is promoted with allelopathic effects by inhibiting the growth and phenotypic performance of native plants, little is known conversely. In this study, the allelopathy effects of a native plant, Humulus scandens (Lour.) Merr., on a typical invasive species Alternanthera philoxeroides (Mart.) Griseb., was investigated by exposing A. philoxeroides seedlings to three chemical solvent extracts (i.e., petroleum ether extract (PE), ethyl acetate extract (EE), and n-butanol extract (NE) of H. scandens root (HR). The three chemical extracts inhibited the growth, stem length, node number, leaf number, leaf area, and root number, and increased malondialdehyde (MDA) content of A. philoxeroides seedlings, which indicated that the extracts inhibited the plant growth by damaging the membrane system of leaves. And the synthetical effect of allelopathy (SE) index indicated that EE had the greatest inhibition on the growth of A. philoxeroides. Fifty compounds were identified from the three extracts of HR using GC-MS analysis, among which 5 compounds (dibutyl phthalate, stigmasta-3,5-diene, 2,6-Di-tert-butylphenol campesterol, and neophytadiene) were identified from H. scandens root extracts for the first time. And n-hexadecanoic acid exists in all three extracts. The findings of the present study provide a novel method to potentially control the invasion of A. philoxeroides. However, field monitoring under natural conditions would be necessary to confirm in practice the results obtained with the bioassays.