The biotechnological process of producing polypeptide and protein feed is superior to traditional fish meal producing process, which has high protein loss rate, high power consumption, high cost, serious pollution and other demerits. The present invention produces polypeptide paste, polypeptide powder, protein paste or protein powder with fresh low value fishes and shrimp and aquatic animal leftover and through the process including the steps of eliminating impurity, steam to eliminate fat, oil-water separation, crushing, sterilizing, enzymolysis, inactivating enzyme, concentration, drying and others. The present invention has the advantages of high protein content in the products, high bioavailability, no environmental pollution, low power consumption, etc. The products have the effects of promoting animal growth, regulating immunity, preventing and treating diseases, etc. and are used mainly in raising animal and as nitrogen source for biological culture.