Metamict zircon crystals have been thermally annealed between 500 and 1800 K and analyzed using infrared and optical spectroscopy in the spectral region of 1400–7000 cm−1. Recrystallization and dehydroxylation via complex proton/OH diffusion, redistribution, and incorporations of additional hydrogen-related species within the crystal structure of zircon occur at temperatures above 700 K in partially metamict zircon and above 1200 K in heavily amorphized material. Thermally induced changes in O-H stretching spectra are different between E || c and E ⊥ c in weakly metamict zircon. The O-H stretching band near 3342 cm−1 (with E ⊥ c) in an untreated sample shifts to 3277 cm−1 at 1200 K, where the frequency of O-H stretching bands with E || c increases. Conversions of hydrogen-related species were observed and extra OH bands were found at temperatures between 1200 and 1600 K. A dramatic change of OH spectra was recorded between 1600 and 1800 K in partially metamict crystals, resulting in additional absorption features (near 3098 and 2998 cm−1 along E ⊥ c). U4+ and U5+ related spectra are also affected by high-temperature annealing. For highly metamict zircon, the U4+ band near 4830 cm−1 shows an increase in intensity above 1200 K. Additional IR bands at 2146 and 2344 cm−1 appear in the spectra of metamict zircon annealed at high temperatures. Their frequencies are consistent with stretching vibrations of CO and CO2.