Thin film bulk acoustic resonator (FBAR) with high quality factor (Q) is preferred for many communication applications. AlN film deposited in conventional FBAR fabrication process is poor, resulting in unsatisfactory device performance. This study demonstrated the comparison of two Si-substrate FBARs, adopting the same AlN deposition process by physical vapor deposition (PVD) method, however using different device fabrication method. Instead of depositing AlN film on Mo/SiO2/Si substrate in existing fabrication process, we deposited AlN directly on Si substrate by PVD to get better crystal quality piezoelectric layer of the FBAR. The full width at half maximum (FWHM) of rocking curve and surface roughness of AlN directly deposited on Si substrate are 1.4° and 1.96 nm, while those of AlN deposited on Mo/SiO2/Si substrate are 8.5° and 5.54 nm, respectively, indicating AlN deposited directly on Si substrate has a better crystal quality than that on Mo/SiO2/Si substrate. The dielectric loss of FBAR using AlN developed on Si substrate decreases from 0.4 Ω to 0.11 Ω leading to the increase of Qm from 470 to 830. By preserving the high quality AlN deposited on Si substate with film transfer method, the FBAR device enjoys an increasing of Q-values as high as 76%.