The effects of ion beam induced atomic mixing and subsequent thermal treatment in Si/C multilayer structures are investigated by use of the technique of grazing incidence X-ray diffraction (GIXRD) and Raman spectroscopy. The [Si (3.0nm)/C (2.5nm)]×10/Si multilayer films were prepared by electron beam evaporation under ultra high vacuum (UHV) environment. The layer thicknesses were measured using in situ quartz crystal oscillator. These multilayer films were subjected to 40keV Ar+ ion irradiation with fluences 5×1016 (low fluence) and 1×1017ions/cm2 (high fluence). The as-prepared and irradiated multilayer samples were annealed at 773K for 1h. The GIXRD and Raman spectroscopy results reveal the formation of different phases of SiC in these multilayer structures. Deposition induced reactions at the nano-structured interface and subsequent room temperature Ar ion irradiation at low fluence result in formation of the hexagonal SiC phase. High fluence Ar+ ion irradiation and subsequent annealing at 773K for 1h leads to precipitation of the cubic SiC phase.