Ion beam induced luminescence from silica glasses containing various OH concentrations was measured to examine the effects of OH and the energy deposition processes on the damage creation under irradiation by H and He ions in the energy range 0.2–3.0MeV. The 2.7eV luminescence center corresponding to the B 2α oxygen deficiency centers was less effectively created in the high-OH silica, where the 1.9eV luminescence originating from the non-bridging oxygen hole centers were prominent. Ion implantation and thermal release experiments showed that MeV ion induced defects trapped hydrogen along its trajectory as a form of Si–H. Annihilation of B 2α centers can be promoted in high-OH silica, by trapping of hydrogen released by the ion induced dissociation of OH. The energy dependence of the initial growth rate of luminescence suggested that the relatively large electronic energy loss of He ions plays roles in excitation and/or production of oxygen vacancies.