Hydrogenated amorphous carbon (a-C:H) films have attracted much attention, because of their excellent physical and chemical properties, such as high mechanical hardness, chemical robustness, a wide variety of optical bandgaps, and so forth. Although an ion bombardment energy has been regarded as essential in the well-know subplantation model, it alone is inadequate especially in complicated reactions of a plasma-enhanced chemical vapor deposition process. In this study, an ion bombardment energy flux (ΓEi) was proposed as a crucial factor to determine chemical compositions and structures of a-C:H films. To obtain the amounts of ΓEi, electron densities, hydrogen (H) excitation temperatures, and negative direct current (DC) self-bias voltage (-VDC) were measured. The deposition rate increased, and sp2-C clusters incorporation was induced by the ΓEi. With increasing ΓEi, photoluminescence (PL) backgrounds in Raman spectra decreased, while spin densities in electron spin resonance (ESR) measurements increased. These results suggested the H content of a-C:H film decreased depending on the amount of ΓEi. The ΓEi is one of the crucial factors to determine the properties of the a-C:H films.