Because of the complex plasma reactions and chemical structures of polymers, it is difficult to construct nitrogen functionalities controllably by plasma technology to attain the desirable biological outcome and hence, their effects on bone cells are sometimes ambiguous and even contradictory. In this study, argon plasma treatment is utilized to convert complex molecular chains into a pyrolytic carbon structure which possesses excellent cytocompatibility. The pyrolytic carbon then serves as a platform to prepare the desired nitrogen functionalities by nitrogen and hydrogen plasma immersion ion implantation. Primary, secondary, and tertiary amine groups can be produced selectively thus minimizing the chemical complexity and creation of multiple types of nitrogen functional groups that are often obtained by other fabrication methods. As a result of the excellent control of the nitrogen functionalities rendered by this plasma technique, the effects of individual nitrogen functionalities on the cytocompatibility and upregulation of bone marrow-derived mesenchymal stem cell (BMSC) osteogenesis can be investigated systematically. The tertiary amine functionalities exhibit the optimal efficiency pertaining to the modulation of the biological response, enhancement of osteogenesis related gene/protein expression, and calcification of the contacted BMSCs. Our results demonstrate that simple plasma technology can be conveniently employed to create the desirable nitrogen functionalities on orthopedic polymers to facilitate osseointegration and mitigate foreign body reactions.