The invention relates to a method for preparing protein peptide by carrying out enzymolysis on marine low-value small fishes by squid visceral enzyme. The method takes the marine low-value small fishes as a raw material, and comprises the steps of unfreezing, carrying out enzymolysis on the substrate small fishes by the squid visceral enzyme after homogenate treatment, and controlling the solid-to-liquid ratio, the temperature, the pH and the enzymolysis time in the enzymolysis process; after that, carrying out enzyme deactivation and concentration to obtain protein peptide paste, or carrying out spray drying treatment on the protein peptide paste to obtain protein peptide powder. The method has the advantages of being simple in technology, low in production cost, high in yield of finished products, suitable for industrial product, etc. The method not only reduces the dosage of industrial protease, but also enables the protein resource to be comprehensively utilized, avoids the environmental pollution and realizes the industrial application of the squid visceral enzyme.