The joint of Carbon fiber reinforced thermoplastic (CFRTP) and aluminum (Al) alloy can combine the excellent properties of the two materials, especially in the transportation track, aerospace and other fields where lightweight needs to be considered. Welding is a common connection technology, which has the advantages of high connection quality and good sealing. However, due to the differences in physical and chemical properties of dissimilar materials, the welding joint has low compatibility and poor weldability, and the current welding process conditions are not clear about the microscopic connection mechanism of the welded joint. Therefore, in this study, Molecular dynamics (MD) simulation method was used to explore the microscopic mechanism of the welding process of Carbon-fiber-reinforced Polyamide 66 (CFRPA66) and Al alloy. By simulating the motion and interaction between PA66 molecule of CFRPA66 substrate material and Al atom in welding process, the molecular motion law of welding interface was analyzed. The results show that the changes of temperature and pressure during the welding process have significant effects on the atomic diffusion and bonding behavior at the interface between PA66 and Al alloy. At 10 ps, the interface model at 550 K presents the maximum absolute value of interaction energy under different temperatures, and the interface model at 1.5 MPa presents the maximum absolute value of interaction energy under different pressures. The simulation results provide a theoretical basis for optimizing the welding process of CFRPA66 and Al alloy, and lay a foundation for further improving the industrial application of CFRTP/ Al alloy composite joint.