The invention relates to a method for preparing 
fish oil ethyl ester by 
microwave esterification and purifying ethyl eicosapentaenoate, which comprises the following steps: adding 
fish oil, absolute 
ethanol and catalyst concentrated 
sulfuric acid into a reaction vessel, and heating under 
reflux in a 
microwave reactor to convert free 
fatty acid into 
fatty acid ethyl ester; after the reaction is carried out for 10-30 minutes, removing excessive 
solvent and catalyst from the product, and 
drying to obtain the 
fish oil fatty acid glyceride of which the 
acid value is smaller than 2; preparing the pre-esterified fish oil, absolute 
ethanol and catalyst KOH into a KOH-
ethanol solution, adding the KOH-ethanol solution into the reaction vessel, and heating under 
reflux in the 
microwave reactor to carry out the ester exchange process; and after the reaction is carried out for 5-15 minutes, stratifying the product by standing or centrifuging, removing the understratum 
glycerol, removing the excessive ethanol and catalyst, and 
drying to obtain the ethyl eicosapentaenoate. The invention adopts two-stage vacuum rectification: light components with lower 
boiling point than ethyl EPA (eicosapentaenoate) are removed in the primary rectification 
tower; and the component subjected to light component removal enters a secondary rectification 
tower to separate the ethyl EPA from ethyl DHA, thereby obtaining the ethyl EPA with the purity of higher than 97%.