The invention discloses a method for integrated extraction of a plurality of biologically active ingredients in a soft-shelled turtle. The method comprises the following steps: S1, adding a complex protease A into a soft-shelled turtle crushed material liquid for enzymolysis; S2, filtering the soft-shelled turtle enzymolysis product, separating soft-shelled turtle crushed bones and a soft-shelledturtle meat liquid product, carrying out centrifugation to obtain a water-phase product of soft-shelled turtle meat and an oil-phase product of the soft-shelled turtle meat; S3, removing the fishy smell of the water-phase product of soft-shelled turtle meat, and carrying out decoloration, fine filtering, concentration and drying to obtain the soft-shelled turtle meat oligopeptide powder; S4, steaming a soft-shelled turtle crushed bone liquid, carrying out filtering to obtain a bone residue and a crushed bone liquid product, carrying out centrifugation to obtain a protein solution of soft-shelled turtle bones and an oil-phase product of the soft-shelled turtle bones; S5, adding a complex protease B into the protein solution of the soft-shelled turtle bones for enzymolysis to obtain a soft-shelled turtle bone protein enzymolysis product; S6, removing the fishy smell of the soft-shelled turtle bone protein enzymolysis product, and carrying out decoloration, fine filtering, concentration and drying to obtain oligopeptide powder of the soft-shelled turtle bone protein; S7, treating the bone residue to obtain soft-shelled turtle shell powder; and S8, mixing the oil-phase product of the soft-shelled turtle meat and the oil-phase product of the soft-shelled turtle bones to obtain soft-shelled turtle oil. According to the method provided by the invention, the soft-shelled turtle resources can be fully utilized, and resource waste is avoided.