Achieving strong joining of aluminum alloy to carbon fiber thermoplastic composites (CFRTP) using laser heating was an essential method to reduce the weight of structure and save energy. In current study, a silane coupling agent was adopted on the aluminum alloy surface to improve the bonding strength of the laser joining of aluminum alloy to CFRTP. Substrate characteristics of the aluminum alloy after treatment including surface morphology, surface roughness and wettability as well as chemical composition were then studied. For comparison, identical experiments were also performed for the polished and sanded aluminum alloy. Compared to the aluminum alloy polished, the surface roughness of aluminum alloy sanded and silane treated was increased, whereas the wettability was both decreased. The rougher surface led to a worse wettability of aluminum alloy surface for these two specimens. In addition, the detected organo-functional group for the latter was also responsible for the increase of water contact angle on the aluminum alloy surface. Compared to the polished specimens, the tensile shear force of joints for sanded and silane-treated substrates averaged 1106.9N and 2959.4N respectively, which represents a respective increase of 1.2 times and 3.3 times than the polished state. Correspondingly, the tensile shear strength of joints was 6.3MPa and 16.8MPa, which was increased by 1.1 times and 2.9 times, respectively. The improved mechanical interlocking induced by increasing the surface roughness in both sanded and silane treated cases was considered to strengthen the bonding strength at the interface. Moreover, for the joints fabricated by aluminum alloy silane treated and CFRTP, the remarkable enhancement of joint strength was also related to the formation of silane coupling film on the aluminum alloy surface. The tensile shear properties of joints were also found to have a positive influence in increasing the adhesion amount of CFRTP on the fractured surface of aluminum alloy. Finally, the silane treatment was expected to play a significant role in joining aluminum alloy to CFRTP.