Consumption of food containing n-3 PUFAs, namely EPA and DHA, are known to benefit health and protect against chronic diseases. Both are richly found in marine-based food such as fatty fish and seafood that are commonly cooked prior to consumption. However, the elevated temperature during cooking potentially degrades the EPA and DHA through oxidation. To understand the changes during different cooking methods, lipid profiles of raw, boiled, pan-fried and baked salmon were determined by LC-MS/MS. Our results showed that pan-frying and baking elevated the concentration of peroxides in salmon, whereas only pan-frying increased the MDA concentration, indicating it to be the most severe procedure to cause oxidation among the cooking methods. Pan-frying augmented oxidized products of n-3 and n-6 PUFAs, while only those of n-3 PUFA were elevated in baked salmon. Notably, pan-frying and baking increased bioactive oxidized n-3 PUFA products, in particular F-4t-neuroprostanes derived from DHA. The results of this study provided a new insight into the application of heat and its effect on PUFAs and the release of its oxidized products in salmon.