Two types of bilayer films were constructed on silicon substrates by a two-step self-assembly strategy. 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (TA) was chosen to create underlayer with amino-terminated surface, then n-octanoic acid (nOA) and perfluorooctanoic acid (PFOA) were chemically grafted to the amino-derivatized substrates, respectively, to construct CH3- or CF3-terminated bilayer film, denoted as TA-nOA and TA-PFOA, respectively. The formation and surface properties of the films were evaluated by ellipsometry, contact angle goniometers, X-ray photoelectron spectroscopy, and atomic force microscope (AFM). The nano- and micro-tribological properties of TA-nOA and TA-PFOA bilayers were comparatively investigated via AFM and ball-on-plate tribometer, respectively. Results show that these two types of bilayer films exhibit good anti-adhesive and friction-reducing properties, and TA underlayer enhances the stability of these films through interchain hydrogen bonding. At nanoscale, TA-PFOA film exhibits lower adhesion and friction force because of -CF3 terminals with lower work of adhesion. However, the micro-tribological property of TA-PFOA is inferior to that of TA-nOA film. This could be attributed to the fact that -CF3 terminal groups with larger size tend to form less-ordered structure. Moreover, larger terminal groups lead to more energy dissipation during sliding.