The invention provides a method for extracting high-purity omega-3 polyunsaturated fatty acid phospholipids from shrimp heads. The method comprises the steps of homogenizing the shrimp heads, and carrying out enzymolysis by complex enzymes; carrying out solid-liquid separation, adding the solid part into an alkaline ethanol solution, carrying out ultrasonic-assisted extraction, filtering and concentrating to obtain an extract; and dissolving the extract, then carrying out polystyrene gel column chromatography, carrying out thin-layer chromatography detection analysis in combination with an eluent, carrying out reduced pressure condensation, washing by an ice ethanol solution, and then drying to obtain high-purity phospholipids. According to the method, the operation is simple, the extraction process is simple and easy to operate, the fixed adsorption amount of column chromatography fillers is few, repeated use can be achieved, the temperature is not more than 50 DEG C, the physiological activity of phospholipids cannot be damaged, and the purity of the extracted phospholipids is more than 95%. Meanwhile, the invention opens up a new approach for high-valued comprehensive development and utilization of marine product processing wastes, and raw materials are not limited in a certain source and can derive from multiple marine animal processing wastes.