Abstract Four typical Brønsted acidic ionic liquids (BILs) and concentrated sulphuric acid (H 2 SO 4 ) were used to catalyze the transesterification of fish oil with ethanol to produce fatty acid ethyl ester (FAEE) in this work. The experimental results show that the imidazole BILs lead to fewer side reactions and higher product quality than H 2 SO 4 . Molecular dynamics (MD) simulations indicate that [PSMim][HSO 4 ] molecules can be enriched at the interface and enhance the contact of eicosapentaenoic acid triglyceride (EPATG, a typical component of fish oil) and ethanol. And ester groups of EPATG tend to expose more to ethanol in the BILs system, which facilitates the occurrence of transesterification. However, H 2 SO 4 has no positive effect on the distribution of the two reactants. For the transesterification, the interfacial property affects the catalytic activity a lot, instead of catalyst acidity. Also, the reaction rate is accelerated, obviously, by ultrasound‐led liquid–liquid phase emulsification.