ScAlN thin films were first prepared on Si (100) substrate by pulsed DC magnetron sputtering. Then, GaN thin films were epitaxial grown on Si (100) substrate with metalorganic chemical vapor deposition (MOCVD) by using ScAlN as the buffer layer. The influence of the thickness of ScAlN buffer layer on ScAlN buffer layer and GaN epitaxial layer is investigated by high resolution Xray diffraction, atomic force microscopy (AFM) and Raman spectroscopy. The results show that the thickness of ScAlN buffer layer is an important factor affecting the crystal quality of GaN thin films. With the increase of ScAlN thickness, the full width at half maximum (FWHM) of ScAlN (002) Xray diffraction rocking curve continues to decrease, and the FWHM of GaN (002) Xray diffraction rocking curve first decreases and then increases. When the thickness of ScAlN buffer layer is 500nm, the crystal quality of GaN is the best, the FWHM of GaN (002) Xray diffraction rocking curve is 0.38°, and the tensile stress calculated by Raman spectrum is 398.38MPa.