The fatty acid compound ingredients in fish oil capsule bought from market were studied. Through esterification reaction, using hexane as solvent with direct injection, the fatty acid methyl ester composition was separated by gas chromatography-mass spectrometry and analyzed the composition by NIST assisted search tool. The results showed that fish oil capsule was mainly composed of 21 kinds of fatty acids, including palmitic acid, palmitoleic acid,oleic acid, DHA, EPA. The relative contents of the fatty acids were calculated by area normalization method. The content of unsaturated fatty acid was close to 70%. The method is simple and fast, which can provide reference for the similar products.