Interaction of organic polymer surfaces with energetic reactive ions during etching processes by hydrogen–nitrogen plasmas has been investigated microscopically with the use of classical molecular dynamics (MD) simulations. Especially examined in the present study are interactions of atomic-nitrogen, molecular-nitrogen, or ammonia beams with a polyparaphenylene (PPP) surface and the resulting surface modification. It has been observed in the simulations that, when reactive atomic-nitrogen (N) beams are injected into a PPP surface, a carbon nitride layer with carbon–nitrogen bonds of higher bond orders (i.e., bonds containing π bonds) tend to be formed and it also acts as a source of carbon-nitride clusters for sputtered species. This observation is consistent with the fact that excessive supply of nitrogen to a carbon nitride film makes the film structurally weak as nitrogen atoms tend to break up carbon chains. On the other hands, when ammonia (NH₃) beams are injected, carbon–nitrogen single bonds (i.e., σ bonds only) are more likely to be formed since hydrogen atoms would efficiently terminate π bonds should they be formed.