Abstract: As high-end manufacturing advances towards lightweight and high-performance directions, the efficient joining technology of heterogeneous materials has become critical in industries including rail transportation and aerospace. The demand for heterogeneous lightweight structures composed of Al and carbon fiber reinforced thermoplastic (CFRTP) is increasingly intense. To achieve high-strength joining between the two materials, based on the fused deposition modeling (FDM) technology, carbon fiber-reinforced nylon 6 (CF-PA6) filaments were directly printed on the surface of 6061Al with a thickness of 1.5 mm, thereby realizing the integrated manufacturing of Al/CFRTP composite structures. The influence mechanisms and interfacial bonding mechanisms of printing temperature and surface microtextures on 6061Al/CF-PA6 FDM-printed joints were investigated. The results show that the temperature determines the melting state and wetting-spreading properties of the resin, thereby directly affecting the interfacial bonding strength. For direct printing at 270 ℃, the joint’s tensile shear force is 885 N, and the tensile-shear strength reaches 2.2 MPa. To further improve the joint strength, microstructures were fabricated on the surface of Al using a nanosecond pulsed laser. The results show that the microstructures can increase the surface roughness and promote the wetting and spreading of the molten resin on the surface of Al. Under optimized process parameters, the resin can fully fill the microstructures on the surface of Al. The mechanical interlocking effect at the joining interface effectively improves the performance of the joint. The tensile shear force of the joint is 1 764 N, and the tensile-shear strength reaches 4.4 MPa.