Molecular dynamics simulations were performed to examine the amine formation in carbon-based polymer films deposited by plasma-enhanced chemical vapor deposition (PECVD) with methane (CH4) and nitrogen (N2) gases. In the simulations, the interactions between the deposited film surface and incident precursors were examined, where nitrogen species were assumed to be supplied only as amino radicals (NH2) such that the amount of primary amine (−NH2) could be maximized in the deposited film. Carbon was supplied as CH2 or CH3 radicals as well as CH2+ or CH3+ ions with an ion kinetic energy up to 100 eV, as typical in such PECVD experiments. It has been found that, even under such “ideal” conditions for the maximum primary-amine content, hydrogen (H) atoms of incident NH2 radicals tend to be transferred to surrounding C atoms in the polymerization process, leaving a relatively small amount of primary amine (the concentration ratio of primary amino groups NH2 to nitrogen atoms N ∼10%) in the deposited polymer films. The simulation results indicate that an increase of NH2 radicals in the gas phase of PECVD hardly increases the primary-amine content in the deposited films and, therefore, the primary-amine content may not depend strongly on the plasma conditions as long as a sufficient amount of nitrogen and hydrogen is supplied during the plasma polymerization process. The primary-amine content predicted by the simulations was found to be consistent with earlier experimental observations.