The interfacial bonding strength in Fiber Reinforced Polymer (FRP) is critical for the mechanical properties of materials. A microdroplet technique is designed to measure the Interface Shear Strength (IFSS) between single fibers and matrix polymers. In this study, the IFSS measurements between non-polar/polar polymers and carbon fibers were investigated by means of microdroplet technique. After compounding the non-polar polypropylene (PP) with polypropylene-graft-maleic anhydride (PP-g-MA), the results show that the IFSS of PP are enhanced from 8.8 MPa to 16.4 MPa. Therefore, the introduction of the polar functionality on the polymer improved the interfacial bonding strength. Two types of polymers, polycarbonate (PC) and polyamide (PA), were further studied to understand the effect of functionalities on the polymers. Our results reveal that PA results show higher IFSS than PC. This indicates that the amide groups (O=C-N) on PA form stronger chemical bonds with the carbon fiber compared to the carbonate groups on PC.