WithagreatdifferenceintherapeuticeffectsofMahuang(MH,thestemsofEphedrasinica)andMahuanggen(MHG,therootsofEphedrasinica),chemicaldifferencesbetweenMHandMHGshouldbeinvestigated.Inthepresentstudy,gaschromatography-massspectrometry(GC-MS)-basedplantmetabolomicswasemployedtocomparevolatileoilprofilesofMHandMHG.TheantioxidantactivitiesofvolatileoilsfromMHandMHGwerealsocompared.32differentialchemicalmarkerswereidentifiedaccordingtothevariableimportanceintheprojection(VIP)valueoforthogonalpartialleastsquaresdiscriminantanalysis(OPLS-DA)andPvalueofMann-Whitneytest.Amongthem,chemicalmarkersoftetramethylpyrazine(TMP)andα-terpineolwerequantified.TheircontentsweremuchhigherinmostMHsamplescomparedwithMHG.TheantioxidantassaydemonstratedthatMHhadsignificantlyhigherfreeradical-scavengingactivitythanMHG.AlthoughMHandMHGderivedfromthesamemedicinalplant,therewasmuchdifferenceintheirvolatileoilprofiles.MHsampleshadsignificantlyhighercontentoftworeportedpharmacologicallyimportantchemicalmarkersofTMPandα-terpineol,whichmayaccountfortheirdifferentantioxidantactivities.