Abstract: A method applying gas chromatography-ion trap mass spectrometry (GC/MS) for the simultaneous analysis of diethyl 3-(2,4-dimethoxyphenyl)allylmalonate isomers is described. The diethyl 3-(2,4-dimethoxyph-enyl)allylmalonate mixture of isomers was prepared by the decarboxylative Heck reaction of 2,4-dimethoxybenzoic acid with diethyl 2-allylmalonate firstly, and then was analyzed by GC/MS in Electron ionization (EI) and Chemical ionization (CI) full-scan mode. Two components were isolated by gas chromatography, and identified as isomers from the determination of the molecular ions. Next, the isomers were analyzed by tandem mass spectrometry (MS/MS) mode. Through the analysis of different cleavage fragments of the isomers in MS/MS mode, mass spectrometric fragmentation pathways of the isomers were discussed. The structures of two isomers were determined on the base of different mass characteristic fragmentation pathways. This new method of identifying isomers is a time-saving, economical and effective method, which could provide reference for analysis and identification of this kind of compounds.