Abstract: The thermodynamic parameters of megastigmatrienone E/Z isomers are calculated in gas phase by MP2 and B3LYP methods respectively.A megastigmatrienone flavor sample is analyzed by four types commonly used capillary gas chromatographic columns.The analysis and calculation results show that the elution order of megastigmatrienone E/Z isomers are exactly the same as (4,7E,9)-,(4,6Z,8Z)-,(4,6Z,8E)-,(4,6E,8Z)-,(4,6E,8E)- megastigmatrienone in turn by DB-WAX,DB-FFAP(identical to SGE BP-21),HP-5MS and RXi-5sil MS columns.The molecular energies of synthesized megastigmatrienone isomers naturally predetermine their relative percentage.For megastigmatrienone flavor samples synthesized by different mechanisms and routes,the percentages of (4,6Z,8E)- and (4,6E,8E)- are dramatically higher than that of (4,6Z,8Z)- and (4,6E,8Z)- isomers,which are consistent with the Boltzmann population in gas phase.The theoretical calculation results agree well with the experimental elution order and percentage of megastigmatrienone E/Z isomers.It may play roles on both qualification and quantification for isomers of megastigmatrienone in flavors.