In this work，entropy minimization algorithms was used to deal with two GC-MS co-eluted peaks got from rose and Arabian jasmine essential oils，and the pure spectra of components inside co eluted peaks were obtained.Identification of those reconstructed components was done by NIST library matching，retention index comparison and MS fragments analyses.Two isomers’ pure spectra were found from each co-eluted peak from rose essential oil and Arabian jasmine essential oil.The results showed that the unknown isomers were successfully identified from the mixture spectra using the entropy minimization algorithm，and the study is very helpful for analyzing isomers in different mixtures.