The effects of Fe-ion irradiation on the crystal structure and superconducting properties of MgB2 thin films were investigated. Pristine samples were prepared using hybrid physical-chemical vapor deposition (HPCVD), and ion irradiation was performed at three different doses of 5 × 1013, 1 × 1014, and 2 × 1014 ions/cm2. The measured temperature-dependent resistivity showed that as the irradiation dose increased from pristine to most irradiated, the superconducting critical temperature, Tc, significantly decreased from 38.33 to 3.02 K. The crystal structures of the films were investigated by X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) measurements. The results showed that the higher the dose, the greater the change in crystal structure, such as the lattice constant and bond length. This suggests that the destruction of the crystal structure at higher doses leads to the degradation of superconductivity in the irradiated MgB2 thin films. Raman spectroscopy showed that the electron-phonon coupling constant decreased with increasing irradiation dose, which was directly related to the reduction of Tc in the samples. The optical conductivity indicates that the charge-carrier density of the σ-band plays an important role in the superconductivity of ion-irradiated MgB2.