Although the triglyceride form is the natural form of fish oil found in fish, the ethyl ester form of fish oil, which is used during processing to save costs, is also present on the market. In this study, fatty acids and lipids were determined using gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–linear ion trap mass spectrometry (LC–LIT/MS), respectively, according to developed methods. The identification of fatty acids was based on the mass spectral characteristics and equivalent chain lengths. However, the fatty acid contents of both forms of fish oils are quite similar. The application of the LC–LIT/MS method for the structural characterization of triacylglycerols (TAGs) and the mechanism of LIT/MS fragmentation are also discussed. Neutral losses of CH2=CH2 (m/z 28) and CH3CH2OH (m/z 46), which are LIT/MS characteristics of ethyl ester from fish oil, were found for the first time. The triglyceride form of fish oils was easily and accurately identified using fingerprint chromatography. In conclusion, lipid analysis combined with LC–LIT/MS showed an improved capability to distinguish between types of fish oil.