A method for producing a site-specifically modified protein based on new carbon-carbon bond formation is disclosed, including the following three steps (marking, activation, and coupling steps): (a) marking of the modification site by incorporating a specific amino acid into a selected position of a target protein; (b) activation of the marked site; and (c) coupling of various post-translational modification (PTM) moieties or other chemical groups onto the activated site to obtain a site-specifically modified protein. The method for producing a site-specifically modified protein can incorporate desired diverse chemical groups including post-translational modification (PTM) moieties into a designated site in a target protein through a new carbon-carbon bond. Furthermore, the modified protein having a site-specific PTM exhibits the same chemical and functional properties as that of a target protein present in cells. Thus, the present invention is useful for studies of cellular proteins, human diseases including cancers and neurodegenerative diseases, and new drug discovery.