Understanding of lipid oxidation mechanisms (e.g., auto-oxidation and photo-oxidation) in foods and cosmetics is deemed essential to maintain the quality of such products. In this study, the oxidation mechanisms in foods and cosmetics were evaluated through analysis of linoleic acid hydroperoxide (LAOOH) and linoleic acid ethyl ester hydroperoxide (ELAOOH) isomers. Based on our previous method for analysis of LAOOH isomers, in this study, we developed a new HPLC-MS/MS method that enables analysis of ELAOOH isomers. The HPLC-MS/MS methods to analyze LAOOH and ELOOH isomers were applied to food (liquor) and cosmetic (skin cream) samples. As a result, LAOOH and ELAOOH isomers specific to photo-oxidation, and ELAOOH isomers characteristic to auto-oxidation were detected in some marketed liquor samples, suggesting that lipid oxidation of marketed liquor proceeds by both photo- and auto-oxidation during the manufacturing process and/or sales. In contrast, because only LAOOH and ELAOOH isomers specific to auto-oxidation were detected in skin cream stored under dark at different temperatures (−5 °C–40 °C) for different periods (2–15 months), auto-oxidation was considered to be the major oxidation mechanism in such samples. Therefore, our HPLC-MS/MS methods appear to be powerful tools to elucidate lipid oxidation mechanisms in food and cosmetic products.