We demonstrate the possibility of laser-assisted phase transformations in thin layers of SiOx from the amorphous nonstoichiometric phase into a nanocomposite layer with Si nanocrystals embedded in the silicon-oxide matrix. The formation of Si nanoparticles (NPs) in SiOx films occurs due to their irradiation with nanosecond pulses of a Nd+3:YAG laser with base wavelength λ = 1.064 μm and the second harmonic λ = 0.532 μm. The nanostructurization of the surface in the form of nanoparticles with mean sizes varying within the range 5–85 nm was detected with the help of atomic force microscopy and optical transmission spectra. The sizes of nanoparticles and their surface distribution depend on the intensity of the laser and its wavelength λ. We determined the mechanism of formation of Si nanocrystals by laser-induced thermal shocks. By analyzing the results of atomic force microscopy, as well as the data of Raman and polarization-modulation spectroscopies, we detected the increase in the amount of single-crystal phase in the film of CNx–Ni nanocomposite with simultaneous increase in the sizes of CNx–Ni nanoparticles caused by the action of laser pulses. The mechanism of laser-stimulated nanocrystallization is proposed. This mechanism is based on the local annealing of the CNx shell as a result of laser heating of the metallic Ni core of CNx–Ni nanoparticles and a more intense sublimation of the amorphous phase of CNx–Ni due to the lower temperature of dissociation of the CNx shell as compared with the Ni core.