In the present study, pure poly(dimethylsiloxane) (PDMS) polymer and PDMS-detonation nanodiamond (PDMS-DND) composite with 1 wt. % of DND were irradiated under vacuum at room temperature with a 2 MeV proton beam with fluences in the 1013–1015 cm-2 range. Modification of the structures and properties of the pure polymer and the nanocomposite material were monitored as a function of proton fluence. Specifically, the vibrational dynamics of pure PDMS and PDMS-DND nanocomposites, both unirradiated and irradiated samples, were investigated using Raman and Fourier transform infrared spectroscopy (FTIR). The Raman and FTIR spectra of the PDMS and PDMS-DND composites exhibit an overall reduction in intensity of all vibrational bands of the irradiated samples. The changes in relative intensities of the characteristic vibrational bands as a function of irradiation fluence indicate that cleavage of the backbone (Si–O–Si) PDMS chains was most pronounced. Importantly, structural degradation of PDMS-DND composites takes place at an order of magnitude higher fluence than for pure PDMS, indicating the potential of using DND-based polymer composites for application in high radiation environments. The appearance of strong photoluminescence following irradiation was more pronounced for PDMS-DND composites as compared to pure PDMS.