Hydrogen-containing nanocrystalline carbon films (n-C:H) with amorphous-nanocrystalline hydrocarbon composite structures exhibit excellent properties in diverse applications. Plasma-enhanced chemical vapor deposition (PECVD) is commonly employed to prepare n-C:H films due to its ability to create an adjustable deposition environment and control film compositions. However, the atomic-scale growth mechanism of n-C:H remains poorly understood, obstructing the design of the appropriate deposition parameters and film compositions. This paper employs a state-of-the-art hybrid molecular dynamics-time-stamped force-biased Monte Carlo model (MD/tfMC) to simulate the plasma-assisted growth of n-C:H. Our results reveal that optimizing the energy of ion bombardments, deposition temperature, and precursor's H:C ratio is crucial for achieving the nucleation and growth of highly ordered n-C:H films. These findings are further validated through experimental observations and density functional theory calculations, which show that hydrogen atoms can promote the formation of nanocrystalline carbon through chemical catalytic processes. Additionally, we find that the crystallinity reaches its optimum when the H/C ratio is equal to 1. These theoretical insights provide an effective strategy for the controlled preparation of hydrogen-containing nanocrystalline carbon films.