For the development of various molecular nanostructures such as single-molecule electronic circuits, it is very important to fix the molecular components at predetermined positions on a substrate. We report the fixation of the thiol derivatives dodecanethiol and (3-mercaptopropyl)-trimethoxysilane (MPS) on a MoS2(0001) substrate at prefabricated sulfur vacancies. Scanning tunneling microscopy (STM) reveals the selective bonding of thiol groups to the Mo atoms at the vacancy defects. In addition, we report STM tip induced dissociation of the S-C bond, which essentially results in the repair of the vacancy defects with sulfur atoms from the thiols. This is consistent with the high desulfurization reactivity of MoS2. Because of its structure and composition, MPS has a higher dissociation reactivity than that of dodecanethiol.