The invention discloses a method for extracting functional protein peptide from basa fish skin. The method comprises steps of mashing, degreasing, enzymolysis with complex enzyme, isoelectric precipitation, two times of ultrafiltration, nanofiltration and freeze-drying. Complex marine protease is adopted as an enzymolysis agent and assisted by ultrasonic enzymolysis, functional protein peptide obtained through freeze-drying is compound polypeptide, and the amino acid sequence of one polypeptide is SCASVCKAHCRCRARRCGYYVSVFYRGRCYCRCLRC. The method has the beneficial effects that the obtained functional protein peptide and collagen are linked through intermolecular forces and hydrogen bonds, and the functional protein peptide is attached to molecular surface of the collagen and coats the collagen, so that the collagen can be protected from being decomposed by gastric acid and can be promoted to reach connective tissue, cartilage and skin dermis layer of animals.