As a promising alternative to traditional prepreg, carbon fiber/poly(ether ether ketone) (CF/PEEK) hybrid composites have attracted wide public interest for their flexibility and conformability. However, modification methods focused on the hybrid premix have not been previously studied. In the present work, the interfacial strength of the hybrid composite was improved by treating the carbon and PEEK fibers together in a radiofrequency (RF) plasma containing one of the following gases to achieve surface activation: air, Ar, or Ar–air. After plasma treatment, the increased roughness of CF and the grafted chemical groups of CFs and PEEK fibers were propitious to the mechanical interlocking and interfacial strength. Significant interfacial shear strength (IFSS) enhancement was achieved after Ar 1 min, air 1 min plasma treatment. This study offers an alternative method for improving the interfacial properties of CF/PEEK composites by focusing on the boundary layer and modifying and controlling the fiber–matrix interface.