Independent component analysis (ICA) has demonstrated its power to extract mass spectra from over-lapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is pro-posed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively. Independent component analysis (ICA) has demonstrated its power to extract mass spectra from over-lapping GC / MS signal. However, there is still a problem that mass spectra with negative peaks at some m / z will be obtained in the resolved results when there based on a detailed theoretical analysis of the preconditions for ICA and the non-negative property of GC / MS signals, a post-modification based on chemical knowledge (PMBK) strategy is pro-posed To solve this problem. By both both simulated and experimental GC / MS signals, it was proved that the PMBK strategy can improve the resolution effectively.