Abstract In this paper, an epoxy structural adhesive was fabricated by using the high‐performance thermoplastic engineering plastic phenolphthalein‐based polyaryletherketone (PEK‐C) as tougheners, and 4,4′‐diaminodiphenylsulfone (DDS) and 4,4‐diaminodiphenylmethane (DDM) as the curing agents. The effect of PEK‐C on the mechanical properties, microstructure, and adhesive properties of the modified epoxy resin system was investigated. Epoxy structural adhesive with 20 phr PEK‐C exhibited excellent bonding performance and thermal stability. The PEK‐C toughened adhesive presented high shear strength of 31.6 MPa and 27.6 MPa at 120°C and 150°C, respectively. The PEK‐C toughened epoxy structural adhesive was then used to bond CF/PEEK composites, and the effects on the bonding properties of CF/PEEK were investigated. By the combined treatment of sandpaper grinding and corona discharge (80 mesh sandpaper sanding + corona treatment for 30 s), the shear strength of the composite joints is increased to 18.73 MPa. And the shear strength retention rate of the joint was 99.8%. The strategy can be used to fabricate sandwich structures with CF/PEEK as the skin with excellent performance. Therefore, PEK‐C toughened modified epoxy resin is conducive to the enhancement of adhesive properties and has a better performance for the bonding of CF/PEEK materials.