Infrared-emitting phosphors based on transition-metal doping have attracted increasing attention due to their broad emission bands and structural sensitivity. However, controlling and identifying the crystallographic site occupancy of transition-metal ions remains a critical challenge for understanding and tuning their luminescent properties. In this work, we investigate the structure–luminescence relationships in LiGa-based oxide phosphors through crystallographic engineering and site-specific analysis. For Cr-doped LiGaO2, a pressure- and temperature-induced phase transition between the β and α structures is employed to modulate the local coordination environment of Cr3+. The reversible phase transition is further monitored in situ by temperature-dependent high-resolution synchrotron X-ray diffraction. To extend this concept, LiGa5O8 doped with Fe3+, Cr3+, and Ni2+ is systematically studied to elucidate the site occupancy of these transition-metal ions between tetrahedral and octahedral sites. By combining k-space oscillation patterns in synchrotron X-ray absorption spectroscopy (XAS), theoretical spectral simulations of XAS, and density functional theory calculations, the preferential occupation behaviors of Fe3+, Cr3+, and Ni2+ ions are identified and correlated with their distinct infrared luminescent characteristics. These results demonstrate that crystallographic site occupancy plays a decisive role in governing the infrared emission of LiGa-based phosphors and provide valuable guidelines for the rational design of transition-metal-doped infrared luminescent materials.