Homogeneous films from SiOx (x = 1.2, 1.3) were deposited on crystalline Si substrates by thermal evaporation of silicon monoxide in vacuum. A part of the films was further annealed at 1000 °C to grow Si nanocrystals in a silicon dioxide matrix. Homogeneous and composite films with initial x = 1.2 were irradiated by 20-MeV electrons at a fluence of 3.6 × 1015 electrons/cm2 and the effect was compared with that caused by irradiation of films with x = 1.3 at much lower fluence of 2.4 × 1014 electrons/cm2. Transmission electron microscopy, infrared transmission and Raman spectroscopies and spectroscopic ellipsometry were used to get information about the SiOx films composition, nanoparticle crystallinity and space distribution as well as for electron-beam induced changes in the nanocrystal size. The infrared data have indicated that electron irradiation with 3.6 × 1015 electrons/cm2 induced phase separation in the homogeneous films with x = 1.2. Not only silicon nanocrystals but also a small amount of amorphous silicon phase have been detected in the composite films before and after electron irradiation. Nanocrystallite size decrease induced by the electron beam irradiation at a fluence of 3.6 × 1015 electrons/cm2 has been assumed on the basis of the observed changes in the effective refractive index, extinction coefficient and nanocrystallite volume fraction in the composite films.