The structural variations of synthetic zircon (ZrSiO4) single crystals irradiated at room temperature by 280 keV Pb+ ions (with fluences up to 1 × 1015 ions/cm2) were investigated using infrared (IR) spectroscopy. Like metamict zircon whose crystal structure is damaged and amorphized by naturally occurring α-decay events, the Pb+-irradiated zircon crystals show a dramatic decrease in reflectivity. However, no significant decrease in wavenumbers of the stretching vibrations of SiO4 tetrahedra in zircon was detected. The Pb+-implanted zircon exhibits new IR bands, indicating irradiation-induced new vibrations or domains, clusters or phases in addition to SiO2 and ZrO2. IR features consistent with those of Pb silicates (with a divalent state, i.e., Pb2+) are also found in the irradiated sample. This finding implies that some of the radiogenic Pb in natural zircon might not actually reside in the zircon lattice or in ZrSiO4 phases, but form new local domains or clusters. Infrared bands of OH-stretching vibrations were also detected in the irradiated synthetic zircon, which was originally free from OH features prior to the irradiation. These results indicate that H can easily diffuse into the irradiated layer or into irradiated-induced phases to form OH or and hydrous species after the irradiated material is damaged. The type and content of hydrous species vary with irradiation fluences.