The quality of interphase in carbon fibers (CFs) composites makes a key contribution to overall performance of composites. Here, we achieved for the first time the chemical grafting of halloysite nanotubes (HNTs) with amino or carboxyl groups onto the CFs surface aiming to increase composites interfacial strength. HNTs were grafted using 3-aminopropyltriethoxysilane (APS) followed by succinic anhydride treatment, and HNTs with amino groups (HNT–NH2) or carboxyl groups (HNT–COOH) were separately introduced into the interphase of composites. Functional groups of HNTs and fiber surface structures were characterized, which confirmed the modification success. The wettability between the modified CFs and resin have been enhanced obviously based on the improved fiber polarity and enhanced surface roughness by the introduced two functionalized HNTs with the uniform distributions onto fiber surface. Moreover, interfacial properties and anti-hydrothermal aging behaviors of modified methylphenylsilicone resin (MPSR) composites were improved significantly, especially for HNT–COOH grafting. In addition, the interfacial reinforcement mechanisms for untreated and modified CF composites are discussed and compared.