Self-assembled dual-layer films have been expected to be excellent lubricants for micro/nano-electromechanical system (MEMS/NEMS). In this research, a novel self-assembled dual-layer film was prepared on single-crystal silicon surface by chemisorption of perfluorododecanoic acid (PFDA) molecules on 3-aminopropyltriethoxysilane (APS) self-assembled monolayer (SAM) with terminal amino group. The chemical composition, structure and morphology of the film were characterized by measurement of contact angle and thickness with ellipsometric method, and by the means of multi-functional X-ray photoelectron spectrometric (XPS) analysis, and atomic force microscopic (AFM) analysis. The nano- and microtribological properties of the dual-layer film were investigated. The dual-layer PFDA–APS film was hydrophobic with the contact angle for water to be about 105° and the overall thickness about 2.5 nm. Atomic force microscopic images revealed that the APS surface was initially characterized with uncontinuous asperities, the surface became relatively smooth and homogeneous after coating with PFDA film by SAM method. The PFDA–APS film exhibited low adhesion and it greatly reduced the friction force at both nano- and microscale. The film exhibited better anti-wear durability than the lauric acid (dodecanoic acid or LA)–APS self-assembled dual-layer film with same chain length and similar structure. PFDA self-assembled dual-layer film is intended for an application in the lubrication and protection of MEMS at low load.