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GaN films grown on Si substrates by molecular beam epitaxy with different nitridation times have been investigated. The GaN/Si structural and optical properties were evaluated by transmission electron microscopy, X-ray diffraction, atomic force microscopy, and photoluminescence. The effective thermal conductivity of the GaN/Si system was obtained using the photoacoustic technique, and from these results the nitridation time dependence of the interface thermal conductivity (η) can be evaluated using a two-layer model. An optimal nitridation time for which the GaN crystal quality can be improved was obtained. The variation of the parameter η for different nitridation times can be related to the interface phonon scattering process by the presence of disorder at the GaN/Si interface.