The invention belongs to the field of deep processing of garlic, and particularly discloses a method for purifying alliinase by double-water-phase separation. The method comprises the following steps: (1) peeling and precooling garlic squamous bulbs, immersing in a precooled extract, homogenizing, centrifuging, and discarding garlic slag, thereby obtaining the supernate crude enzyme solution; (2) dissolving ammonium sulfate, sodium dihydrogen phosphate or trisodium citrate in a Britton-Robinson buffer solution, oscillating to completely dissolve, adding a PEG (polyethylene glycol) solution, evenly mixing by oscillation, and standing for phase splitting, thereby obtaining a double-water-phase extractant; (3) adding the crude enzyme solution into the double-water-phase extractant, oscillating, centrifuging, and standing for phase splitting; and (4) ultrafiltering the lower phase of the enriched alliinase, and carrying out vacuum freeze drying on the trapped fluid to obtain the alliinase solid. The method is simple to operate, has the advantages of simple apparatuses, time saving, low cost, and higher alliinase purification multiple and enzyme activity recovery rate than the prior art, and can easily implement scale-up production.