Epitaxial cubic (100) 3C-SiC films on a (100) silicon wafer were irradiated at room temperature with 2.3-MeV Si+ or 3.0-MeV Kr+ ions up to a fluence of 1 × 1016 cm−2. The evolutions of the epilayer and the substrate were followed as a function of ion fluence by using micro-Raman spectroscopy, optical absorption, and diffuse reflectance spectroscopy in the UV-visible and near infrared range. Raman spectra evidence the amorphization of SiC films at an estimated dose of about 0.1 displacement per atom (dpa) for both ion irradiations. The narrow peaks of the Raman-allowed TO and LO modes of SiC and Si are recorded in the virgin sample, together with few peaks assigned to zone-edge modes of SiC arising from the intrinsic disorder in the strained films. Those crystal phonon peaks broaden or disappear with increasing fluence. The spectra finally exhibit broad extra peaks assigned to the formation of Si–Si and C–C wrong homonuclear bonds in the local order of the amorphous phase. The optical transmission and diffuse reflectance spectra feature interference fringe patterns in the SiC film that are smoothened out with irradiation due to the matching of refractive indices of the amorphous SiC film and Si substrate. The evolution of the refractive index of SiC and optical gap of Si are deduced from those spectra. The respective roles of ballistic effects and electronic excitations in the radiation damage of both SiC and Si are discussed for those two ions with about the same electronic stopping power and about one order-of-magnitude difference in nuclear stopping power. The damage is dominated by the nuclear collision processes and rather well correlated with the estimated irradiation dose in dpa. Optical spectra show that electronic excitations induce damage recovery of the amorphized substrate below the SiC/Si interface. Raman spectra and optical absorption/reflection spectra yield complementary pictures of the radiation damage.