To investigate the damage profiles of high-fluence low-energy proton irradiation on superconducting materials and related devices, Raman characterization and electrical transport measurement of 40-keV-proton irradiated YBa2Cu3O7−x (YBCO) thin films are carried out. From micro-Raman spectroscopy and x-ray diffraction studies, the main component of proton-radiation-induced defects is found to be the partial transition of superconducting orthorhombic phase to the semiconducting tetragonal phase and non-superconducting secondary phase. The results indicate that the defects induced in the conducting CuO2 planes, such as increased oxygen vacancies and interstitials, can result in an increase in the resistivity but a decrease in the transition temperature TC with the increase in the fluence of proton irradiation, which is confirmed in the electrical transport measurements. Especially, zero-resistance temperature TCO is not observed at a fluence of 1015 p/cm2. Furthermore, the variation of activation energy U0 can be explained by the plastic-flux creep theory, which indicates that the plastic deformation and entanglement of vortices in a weakly pinned vortex liquid are caused by disorders of point-like defects. Point-like disorders are demonstrated to be the main contribution to the low-energy proton radiation damage in YBCO thin films. These disorders are likely to cause flux creep by thermally assisted flux flow, which may increase noise and reduce the precision of superconducting devices.