Poly(ether ether ketone) (PEEK) possesses attractive mechanical and thermal properties but demonstrates poor adhesion. To overcome this disadvantage, in this study, the surface modification of PEEK or PEEK-based carbon-fiber-reinforced thermoplastics (CFRTP) was performed through the Friedel Crafts reaction and successive epoxidation. Under optimized reaction conditions, surface modification was achieved without surface deterioration, and epoxy groups were introduced. The progress of the Friedel Crafts reaction and epoxidation was demonstrated by X-ray photoelectron spectroscopy measurements after fluorine labeling through thiol en reaction and amine addition, respectively. The adhesive strength between CFRTP and epoxy adhesives was increased to 23.5 MPa, and cohesive fracture of epoxy adhesives, rather than interfacial peeling, occurred. In addition, compared with conventional plasma treatment, the durability of the modified surface and thickness of the modified surface layer increased. Therefore, we succeeded in modifying the surface properties through the epoxidation of the PEEK surface.