The chemical bonding of substrate and adhesive occurs in thermoplastic adhesive bonding, and the molecular deformation caused by the difference in chemical bonding affects the adhesive properties. Therefore, it is essential to investigate the correlation between the molecular deformation of interphase and the strength change behavior. As adhesive bonding involves the combination of two materials with different coefficients of thermal expansion, it is important to analyze the behavior at high temperatures. Therefore, to determine the effects of the molecular deformation of the interphase caused by differences in the adhesive type on the high-temperature performance when adhesive bonding is applied to thermoplastic composites, fusion and adhesive bonding were applied to carbon fiber/polyetherketoneketone thermoplastic composites. The lap shear strength test was conducted at three different temperatures to evaluate the adhesive performances. Scanning electron microscopy was used to determine the fracture mode and the molecular deformation of the interphase was analyzed by Fourier transform infrared spectroscopy. Temperature does not affect the strength of fusion bonded composites. When polyetheretherketone is used as an adhesive, the strength decreases as the temperature increases. When polyetherimide is used as an adhesive, the strength first increases at [Formula: see text]C and then decreases at [Formula: see text]C. The amount of C–O–C and C=C bond formation, diphenyl ketone group, and imide carbonyl group in the interphase followed the same trend as the strength.