The present invention discloses a separation method for high-content omega-3 fatty acid ethyl ester from ethyl ester type crude fish oil. According to a method in the prior art, the dissolved amount of a raw material in a non-polar solvent is small, so that the charge amount of the raw material in a reaction is small, the production efficiency is low, and the production cost is high. According to the method of the present invention, a polar solvent is used as a raw material solvent, a non-polar solvent is used as a detergent, and a solvent that is the same as the raw material solution is used as an extractant in an extraction section; and according to a liquid-liquid extraction principle, by adopting multistage countercurrent technology, high-purity omega-3 fatty acid ethyl ester is prepared and purified from fish oil with different purity levels of omega-3 fatty acid ethyl ester. The method disclosed by the present invention is simple in operation, small in three-waste discharge and easy for industrial production.