Abstract: OBJECTIVE To analyze the fatty acid composition of 4 batches of imported cod liver oil samples, 6 batches of simulated natural cod liver oil samples and 16 batches of cod liver oil sampling from the domestic pharmaceutical market by gas chromatography(GC) and gas chromatography-mass spectrometry(GC-MS). METHODS The sample pretreatment was achieved through methyl esterification in the presence of KOH-MeOH, while the derived fatty acid methyl esters(FAMEs) were separated polar capillary column. The major fatty acid in cod liver oil were identified by located of the retention time of reference substance combined with NIST library searching of GC-MS. Palmitic acid, palmitoleic acid, oleic acid, linoleic acid, eicosapentaenoic acid(EPA), docosahexaenoic acid(DHA) and other 14 kinds of fatty acid were identified and quantitative analyzed by the normalization method of peak area. RESULTS The content of the identified 14 kinds of fatty acid in domestic pharmaceutical market cod liver oil samples showed a great difference with the imported cod liver oil and simulation of natural cod liver oil samples. Among them, the relative content of some fatty acid, especially, EPA and DHA in simulated natural cod liver oil and imported cod liver oil samples was much higher than that in the domestic cod liver oil samples. While the content of linoleic acid was as high as 44% in domestic cod liver oil samples, which was 10 times higher than it in the simulation of natural cod liver oil and imported cod liver oil samples. CONCLUSION The composition of fatty acid in cod liver oil samples vary from origin to origin. It suggests that whether the cod liver oil samples have add natural cod liver oil ingredients or not depending on the difference of fatty acid composition.