The growth morphology and mechanism of pentacene films on native Si oxide surface have been studied by using high-resolution electron energy loss spectroscopy (HREELS), X-ray diffraction (XRD), and atomic force microscopy (AFM). Despite the good agreement between our own and the reported XRD results, the previous XRD interpretation that the pentacene molecules are tilt-standing on the substrate cannot explain our HREELS data. The HREELS results show that a substantial portion of the first two layers of pentacene molecules are tilted-standing or randomly oriented, whereas the upper-layer molecules are mostly lying flat to the substrate. AFM reveals that the first two layers of molecules form a flat and smooth surface, but the upper layers show a rough terrace structure with a mean-square roughness equal to the average thickness (without counting the first two layers). This relationship is explained by a theoretical model which assumes the pentacene molecules to remain on a particular molecule layer after arrival. The observed film growth morphology may have significant implication on the performance of electronic devices based on pentacene thin films. A plausible explanation was proposed for the discrepancy between the HREELS-indicated and the XRD-derived molecular orientations.