Interfacial structures govern the reliability of metal−thermoplastic hybrid joints used in the aerospace industry. The current work demonstrated by experimental methods and density functional theory (DFT) calculations that introduction of carbon fibers (CFs) enhanced the mechanical properties and weakened the corrosion resistance of polyamide 6 (PA6)/A6061-T6 (6061) joints. The bonding strength of typical PA6/6061 joints was increased by 33.70% with the introduction of CF. However, the differences in intrinsic work functions of the CF and various phases within 6061 led to the formation of serious cracks at CFRPA6/ 6061 interfaces and heavy corrosion on 6061 surfaces, corresponding to the decreased corrosion resistance of PA6/6061 joints.Herein, we present a potential solution to adjust the welding heat input to enhance metal/thermoplastic interfacial reliability. With a rotation speed of 400 mm/min during friction lap joining (FLJ), the fabricated CFRPA6/6061 joint could achieve a strong interface with high strength (bonding strength = 1.730 kN) and relative corrosion resistance (corrosion rate < 0.1 mm/a). The results provide a reliable explanation for the effect of CF on mechanical properties and corrosion resistance of CFRPA6/6061 joints. Furthermore, the knowledge gained in this work will benefit future research in the optimization of processes to improve the reliability of metal− thermoplastic hybrid structures.