The invention belongs to the technical field of biomedical materials, and discloses a pearl natural active peptide having a whitening efficacy, a method for extracting the pearl natural active peptide from nacre, and an application of the pearl natural active peptide. The pearl natural active peptide is obtained by extracting nanometer pearl powder as a raw material through heating water extraction and ultrasonic concussion conditions based on the full exposure of the effective active components of the nanometer pearl powder, and separating and purifying through technologies comprising ultrafiltration for removing macromolecular substances, membrane separation for removing salts, gel chromatographic purification and the like, and the relative molecular mass of the pearl natural active peptide is accurately detected through high performance liquid chromatography. The pearl natural active peptide has the characteristics of basically zero addition of any reagents in the whole extraction and purification processes, guarantee of the natural activities, and good safety, and can be widely used in the fields of cosmetics and medicines for inhibiting the synthesis of melanin in cells as a whitening agent.