In this paper, a new method based on molecular self-assembly on carbon fiber surface was proposed for the improvement of interfacial properties between fiber and epoxy matrix in a composite system. In order to obtain the controlled interphase, the surface of carbon fibers was first metallized by electroless Ag plating, then was reacted with terminally functionized alkanethiols or aromatic thiols to form Ag-thiolate thin films, which further reacted with epoxy resin to generate a strong adhesion interface. The composition, structure and the morphology of the modified carbon fiber surface were examined by X-ray photoelectron spectroscopy (XPS), surface-enhanced Raman scattering (SERS) and atomic force microscope (AFM), respectively. The results showed that these self-assembly molecules were chemisorbed onto the carbon fiber surface coated with silver via the strong S-Ag bond. In addition, these thiol molecules act as coupling agents between the epoxy matrix and carbon fiber through active functional end-groups, such as –OH, -NH2. The interfacial shear strength (IFSS) of the microcomposites after introduced the controlled interphase using the microbond testing was improved.