Poly(ethylene terephthalate) nanocomposites reinforced with 1 wt% of nanodiamond terminated with carboxylic groups or nanodiamond and 0.3 wt% nanographene platelets were prepared by simple melt blending in a twin-screw extruder to create high-performance polymer nanocomposites for application in high radiation environments. A study of structural modifications introduced by high-energy, 3 MeV proton beam irradiation of poly(ethylene terephthalate) and its nanocomposites was conducted using attenuated total reflectance Fourier transform infrared and Raman spectroscopy, differential scanning calorimetry, and photoluminescence measurements. It was shown that the composite materials containing small concentrations of nanodiamonds or nanodiamonds plus nanographene platelets exhibit improved radiation resistance compared with neat poly(ethylene terephthalate) exposed to proton irradiation under the same irradiation conditions. The nanocomposites containing the combination of nanodiamonds and nanographene platelets exhibited the highest stability. Nanofillers, particularly nanographene platelets, stabilized the amorphous phase and increased the crystallinity of polymer matrix exposed to proton irradiation, preserving polymer conformation, molecular weight distribution, and overall thermal properties of irradiated nanocomposites.