The existence states of the H atoms in hydrogenated diamond-like carbon (a-C:H) films were simulated using a modified REBO II potential function-based large-scale atomic/molecular parallel simulator (LAMMPS) and neutral C and H atom beam impingement. The fraction of the H atoms in the incident source (H-flux fraction) in the source must be considered when investigating the effects of the incident energy combination on the H content and mass density of the films. In simulations a-C:H film deposition using a 15 % H-flux fraction, films with densities of 2.6–2.8 g/cm3 could be obtained, and their H content varied with the incident energy. However, the H contents of films simulated using a 70 % H-flux fraction could be kept in the range of 40–50 at.%. The H atoms in the films preferentially reacted with the C atoms to form CH bonds. Regardless of the incident energy combination used, the total sp3C fraction in the film increased with the H-flux fraction of the source. An incident energy of >36 eV for the H atoms was necessary to form H2 during the film deposition. Instead of being formed in the surface growth zone, H2 molecules were synthesized in the stabilized zone, where a high density of sp3C—Hn was favorable.