The invention belongs to the technical field of bioengineering, and particularly relates to a method for preparing fish head polypeptides by performing enzymolysis on fresh water fish head proteins. The method comprises the following steps: cleaning, pulverizing, adding a dilute alkali solution, carrying out microwave treatment, carrying out coarse filtration, carrying out enzymolysis, inactivating the enzyme, carrying out microfiltration, carrying out ultrafiltration, concentrating and carrying out spray drying. The method has the advantages of high yield, high purity, low solvent consumption and low cost, and can easily implement industrial production. The whole technique has the characteristics of short process, short time, low energy consumption, low pollution, no use of toxic reagents and no pollutant discharge, and achieves the goal of clean production.