Atomistic structures of high-energy ion irradiated GaN were examined using transmission electron microscopy (TEM). Single crystalline GaN substrates were irradiated at cryogenic temperatures with 2 MeV Au2+ ions to a fluence of 7.35×1015 Au/cm2. Cross-sectional TEM observations revealed that damaged layers consisting of amorphous and nanocrystalline phases are formed at the surface and buried depth of the as-irradiated GaN substrate. Atomic radial distribution functions of the amorphous/polynanocrystalline regions showed that not only heteronuclear Ga–N bonds but also homonuclear Ga–Ga bonds exist within the first coordination shell. It was found that the ratio of heteronuclear-to-homonuclear bonds, i.e., the degree of chemical disorder, is different between the surface and buried damaged layers. The alternation of chemical disorder was attributed to the difference in the defect formation processes between these layers.