The present invention relates to a pharmaceutical composition for the prevention or treatment of CFC (cardiofaciocutaneous) syndrome comprising a TGF-β signaling pathway inhibitor or a BMP signaling pathway activator. The treatment of SB-431542 or BMP4 protein was confirmed to increase the ALP activity and bone mineral deposition in the osteoblasts originated from the induced pluripotent stem cells derived from CFC syndrome patients. Thus, the TGF-β signaling pathway inhibitor containing SB-431542 or the BMP signaling pathway activator containing BMP4 protein can be effectively used for the prevention or treatment of CFC syndrome.