Abstract The fishy odor of fish oil, a popular nutritional supplement, affects its quality as well as consumer acceptance and eating experience. An objective or scientific method for analyzing fish oil’s olfactory characteristics is still lacking. This study examined anchovy oil to develop qualitative and quantitative approaches for identifying fishy odor components. Multiple fish oil refining samples were analyzed using gas chromatography-ion mobility spectrometry (GC-IMS). Due to their significant alterations during fish oil refining, low threshold values, and distinct olfactory properties, the unsaturated aldehydes (E)-2-pentenal and (E,E)-2,4-heptadienal and the unsaturated ketone 1-penten-3-one may contribute to the fishy odor. Among the chemicals, (E,E)-2,4-heptadienal was chosen as the marker for developing a method to quantify fishy odor and analyze deodorization samples using headspace solid-phase micro-extraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). The quantitative study of fishy odor in fish oil is a pioneering approach that can help improve quality assurance and refining process.