The possibility of laser-assisted phase transformation in SiOx thin layers from amorphous non- stoichiometry phase to the nanocomposite layer with Si nanocrystalles embedded into silicon oxide matrix was shown. Formation of Si NPs in the SiOx film was occured due to irradiation by nanosecond pulses of the Nd+3: YAG laser with base wavelength, λ = 1,064 μm, as well as second harmonic generation, λ = 0,532 μm. Nano-structurization was manifested with creation of the nanoparticles of sizes from 5 to 85 nm by atom force microscopy images and transmission optical spectra. The nanoparticles sizes and its surface distribution depended on laser intensity I and wavelength λ. The mechanism of Si nanocrystals formation based on laser–thermal shock effect has been determined. From the results of the research of atom force microscopy images, Raman spectra and polarization modulation techniques, the increase in the contribution of the monocrystalline phase in the CNx-Ni nanocomposite film with the simultaneous increase in the size of CNx-Ni nanoparticles due to the pulsed laser action was revealed. The mechanism of laser-stimulated nanocrystallization is proposed, which consists in the local annealing of the CNx shell in the laser heating of the metallic core of the Ni nanoparticle and also due to the superior erosion of the amorphous phase of CNx-Ni due to the lower dissociation temperature of the CNx shell as compared to the Ni core.