In recent years, for the aim of weight reduction of transportation equipment, carbon fiber reinforced thermoplastics (CFRTPs), which have high recyclability and formability, are becoming suitable for mass production. Additionally, with the development of multi-material structures, excellent technologies for joining metal and CFRTPs are required. In present industry, joining between dissimilar materials include adhesive bonding and mechanical joining methods, however, these methods still have some problems, and therefore an alternative bonding method without adhesive and mechanical joining is required for joining CFRTPs and metals. Thus, this study focused on direct bonding between CFRTP and an aluminum alloy, by producing a nanostructure on the surface of the aluminum alloy. The nanostructure penetrates the CFRTP matrix causing an anchoring effect, which results in significant bonding strength improvement. The influence of the nanostructure on the fracture toughness for the directly bonded CFRTP and aluminum was evaluated by static double cantilever beam (DCB) testing. Due to the difference of the thermal expansion coefficients between the CFRTP laminates and the aluminum alloy, significant residual stresses are generated. The effect of the thermal residual stresses on the fracture toughness along with the resulting mode mixity (mode I and II) was calculated. It is found that the thermal stresses introduce a significant mode mixity of the fracture toughness.