Polymer/metal hybrid lightweight structures are increasingly employed in automotive, aerospace and electronics industries. Friction stir welding (FSW) is applied for the effective welding of metals and thermoplastic materials. For the welding of dissimilar materials, due to the significant property differences, it is hard to achieve high strength welded joints with smooth appearance. In this article, the influence of pin length is studied by experiments for the friction stir lap welding (FSLW) of Al alloy and carbon-fiber-reinforced thermoplastic (CFRTP). Tensile tests, OM, SEM and EBSD are carried out to evaluate the welding performance. Results indicate that the joint with smooth surface topography is obtained at the pin length of 2.5 mm with a peak temperature of 250.3 °C and the CFRTP matrix PEI thermal decomposition temperature residence time of 47.6 s. From OM and SEM micro analysis, the width of the bonding area is 3.02 mm and a thin uniform interaction layer is formed in the joint. EBSD confirms that the Al alloy in the stirring zone is refined after recrystallization. It is difficult to form a stacked layered structure in the bottom of joint, so the property of the joint is improved. The tensile strength is 32.9 MPa, which is 63.1% of CFRTP.