The invention discloses a processing method of a protein peptide product from low-value fishes. The processing method comprises the steps as follows; 1) pretreatment; 2) degreasing; 3) fishy smell removing; 4) enzymolysis; 5) dialysis; 6) spray drying; and 7) finished product obtaining. The processing method has the benefits as follows: the prepared protein peptide product from low-value fishes has small molecular weight, has the average molecular weight being 1,200 Da and can be digested and absorbed by the human body easily, and the protein peptide can effectively relax nerves, promote sleep and relieve depression; the protein peptide product has very low fat content, cannot be oxidized to deteriorate easily, has long shelf life and has high protein peptide purity; the content of vitamins and minerals is high, DHA is also contained, the product is high in nutritional value and scientific in matching, and the nerve relaxing effect and the depression treatment effect are improved. The processing method is simple to operate and good in reproducibility, less equipment is required and low in production cost, the low-value fishes are adopted as raw materials, the resources are fully utilized, the added value of the low-value fishes is increased, and the method is suitable for mass production.