The possibility of laser-induced structural transformation of amorphous SiOx thin layers into the SiOx -based nanocomposite layers with increased Si nanoparticles (NPs) has been studied. It was found that the average sizes of silicon NPs depend on the laser intensity (IL) and wavelength (λ). The NPs range of sizes d increase from 1 nm ≤ d ≤ 10 nm in initial films up to 1 nm ≤ d ≤ 35 nm with predominant of the single-crystalline Si NPs in modified SiOx after processing by pulses of the Nd+3: YAG laser (λ = 532 nm) with a pulse duration τ = 10 ns. The structural and topographic changes of SiOx films were studied using field emission scanning electron microscope (FESEM), Energy-Dispersive X-ray Spectroscopy (EDXS), and Raman spectroscopy. The high-frequency shift of the Raman band responsible for the crystalline phase of silicon NPs, caused by the quantum confinement effect, showed an increase in the average of the NPs size with the laser intensity (IL). This is correlated with a decrease of intensity Raman band with a maximum at a vibration frequency at 475 cm−1, which testifies for the decrease of the amorphous phase in the SiOx film with an IL increasing. The correlation between the increase of the average sizes of silicon NPs, the values growing of the stoichiometric index x in SiOx film, and the decrease of the percentage of amorphous silicon was established. The physical mechanisms that explain the growth process of Si NPs are based on the laser thermal shock effect with the following coalescence of Si atoms into NPs and recrystallization of a melted fraction of SiOx film into the NPs with changed sizes have been proposed.