Abstract: Different modes of electron impact (EI), positive chemical ionization (PCI) and negative chemical ionization (NCI) in Gas Chromatography-Mass Spectrometry (GC-MS) determination of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in food are summarized and compared in this paper. Both PCI-MS/MS and EI-MS/MS have high selectivity and sensitivity. PCI-MS/MS has obvious advantages in the analysis of compounds containing nitro or carbonyl groups, while EI-MS/MS has slightly better performance when dealing with dieldrin, endrin, endosulfan and its metabolites. NCI-MS has the highest sensitivity, but weaker anti-interference ability, and is not suitable for the analysis of DDTs and PCBs. In summary, these three mass spectrometry methods, which are complementary and alternative to the routine analysis, can satisfy the requirements of pesticide residue analysis in food by providing good accuracy, good precision and low detection limits.Also it points out that Gas Chromatography showed a superiority in organochlorine compound analysis, but for traditional GC-MS, especially in the EI ionization mode, the spectrum is more complicated because of matrix interference. New ionization modes including the highly selective chemical ionization, will be one of future developments and trends of Gas Chromatography applications in the field of food safety analysis.