Identification of the hydrogen lattice location in crystals is key to understanding and controlling hydrogen-induced properties. Combining nuclear reaction analysis with the ion channeling technique, we experimentally determined the locations of H and D in epitaxial nanofilms of titanium hydrides. It was found that 11 at.% of H are located at the octahedral site with the remaining H atoms in the tetrahedral site. Density functional theory calculations revealed that the structures with the partial octahedral site occupation are stabilized by the Fermi level shift and Jahn-Teller effect induced by hydrogen. In contrast, D was found to solely occupy the tetrahedral site owing to the mass effect on the zero-point vibrational energy. These findings suggest that site occupation of hydrogen can be controlled by changing the isotope mixture ratio, which leads to promising manifestation of novel hydrogen-related phenomena.