Semicrystalline polyethylene terephthalate (PET) foil stacks were irradiated under vacuum and at room temperature with 35 MeV/u Ar ions to fluences ranging from 1×1010 to 5×1012 ions/cm2. Ion induced modifications in crystalline and chemical structures were studied by means of differential scanning calorimetry (DSC), Fourier-transform infrared absorption spectroscopy (FTIR), and X-ray diffractometer (XRD). The DSC and XRD data show a significant loss of crystallinity at the absorbed doses higher than 4.0 MGy. FTIR measurements indicate that the loss of crystallinity of the irradiated PET is related to the scission processes of the main chains at the trans configuration of the ethylene glycol residue. Meanwhile, at the absorbed dose above about 4.0 MGy, bond breaking processes at the para position of benzene are also observed. The benzene ring structures are found to be more stable under irradiation.