Adhesion force measurement by Atomic force microscopy (AFM) is used to investigate the interfacial interaction of the carbon fiber (CF)/epoxy composite for the first time. The epoxy functionalized AFM tip and three types of carbon fibers with different surface chemistry and morphologies were used in this study. Results show that the Bis (3-aminophenyl) phenyl phosphine oxide (BAPPO) modified CF possesses a much larger adhesion force (72.7 nN) than the as-received and de-sized CF (22.5 nN and 17.9 nN, respectively) due to formation of the chemical bonding between the BAPPO modified CF and the epoxy functionalized tip. Single fiber microbond test demonstrates that the interfacial shear strength (IFSS) of BAPPO modified CF/EP composite is 15% and 22% larger than that of as-received and de-sized CF/EP, respectively. This nanoscale manipulation by AFM provides a new avenue to measure the interfacial adhesion between the CF and epoxy at the molecular level.