The invention discloses a processing method of low-value fish protein calcium peptide. The processing technology uses low-value fish bones as raw materials, undergoes deodorization treatment, preparation of fish protein peptides, preparation of fish bone powder, extraction of soluble calcium in fish bone powder, Preparation steps of fish protein calcium peptide Fish protein calcium peptide was prepared. The beneficial effects are: the protein calcium peptide of the present invention is rich in nutrition and comprehensive, and the product has high purity, solves the problem of backlog of raw material fish and waste of resources in the production process of low-value fish, increases the added value of low-value fish products, and has great market development potential; the protein Calcium peptide is non-toxic, non-irritating, and has good solubility in the body. It not only has excellent compatibility with various nutrients including vitamins and antibiotics, and has a synergistic effect, but also the human body can absorb protein calcium peptide through the absorption route of protein peptide, and the absorption speed Fast, 2 to 3 times that of inorganic calcium, easy to be accepted by consumers; the processing technology of the present invention has low production cost, can be designed into fully automatic operation, and has high production efficiency.