Abstract: The optimum conditions and the changes of volatile flavor compounds were studied in each stage of the refining process for the crude fish oil from Snakehead fish viscera. In this study, crude fish oil was extracted from Snakehead fish viscera, and then the degumming, deacidification, and decolorization conditions were optimized by a single factor with acid value and peroxide value as response values. Gas chromatography-ion mobility spectroscopy (GC-IMS) was used to detect the volatiles at different stages of refining fish oil, and the differences in volatiles at the stage of best refining fish oil were investigated by using chemometrics and orthogonal partial least squares discriminant analysis (OPLS-DA) combined with relative odor activity value (ROAV). The results showed that the best refining conditions of Snakehead fish oil were 0.6% phosphoric acid degum, 0.7% excess alkali (NaOH, 4 mol/L) deacidification, 5% active clay decolorization, and the acid value and peroxide value of fish oil were lowest, which were 0.59 mg KOH/g and 2.62 mmol/kg, respectively. A total of 58 volatile flavor compounds were detected by GC-IMS during the refining stage of Snakehead fish oil, among which aldehydes (25) were the most abundant, followed by alcohols (11) and ketones (8). The volatile flavor compound content of degumming oil was the highest, and the volatile flavor compound content gradually decreased with refining. After the deacidification and deodorization stage, the volatile flavor compounds decreased significantly (P<0.05). GC-IMS combined with OPLS-DA and variable importance in projection (VIP) analysis screened out 10 key volatile flavor compounds, as follows: citronellal, (Z)-4-heptenal, butanal, 3-methylthiopropanal, 1-octen-3-ol, n-butanol-M, cis-2-penten-1-ol, 1-penten-3-one, (E)-2-hexene and pyridine. ROAV results showed that (E)-2-nonenal was the major contributor to the flavor of Snakehead fish oil, along with 1-octen-3-ol, (E,E)-2,4-heptadienal, citronellal, n-octanal, (Z)-4-heptenal, hexanal, 3-methylbutanal, propanal, heptanal, 3-methylthio-propanal, 2-hexanone, ethyl pentanoate, 2-pentylfuran and 2-hexenal, which together contributed to the distinctive aroma of Snakehead fish oil. The results showed that refining significantly reduced the content of key volatile compounds in the Snakehead fish oil, and improved the quality of Snakehead fish oil. The results can provide a theoretical basis for preparing low-fishy fish oil in the future.