Synthesis and structural studies of nanocrystalline silicon grown in pulsed laser deposited SiO X films is reported. The effect of high energy heavy ion beam irradiation on these films is studied using 100MeV Ag ions. The structural studies were carried out using micro Raman spectroscopy, GAXRD, FTIR, TEM, HRTEM, SAED and EDX. The occurrence of phase separation in non-stoichiometric silicon oxide by means of ion beam irradiation leading to the formation of silicon nanocrystals in the films is confirmed by the results. HRTEM results reveal the structure of silicon phase formed after ion beam treatment and the particle size can be controlled up to 2–3nm. A detailed analysis by micro Raman and HRTEM studies suggest the presence of crystallite size distribution. The results of GAXRD and SAED confirm the formation of cubic phase of silicon with two different lattice parameters. The studies conclude that the size of the nanocrystals can be controlled by varying deposition and ion irradiation parameters.