Provided are a protein conjugate in which a physiologically active polypeptide is linked to a biocompatible material via a non-peptidyl polymer-coupled fatty acid derivative compound serving as a linker, exhibiting an increased duration of physiological activity compared to natural forms and a preparation method therefor. Since an increase in serum half-life of the physiologically active polypeptide of the protein conjugate, in which the biocompatible material, the non-peptidyl polymer-coupled fatty acid derivative compound, and the physiologically active polypeptide are linked, is proved, the protein conjugate may be widely used in the field of protein drugs.