The composite structure of carbon-fiber-reinforced-thermoplastic (CFRTP) and aluminum alloy can combine the excellent properties of these materials, and has great application potential in rail transit, aerospace and other fields where lightweight needs to be considered. Welding technology has the advantages of strong stability and high sealing, which is a new technology to explore the preparation of CFRTP and aluminum alloy composite structures. However, due to the large 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 bonding mechanism of the welded joint. Therefore, the molecular dynamics (MD) simulation method was adopted in this study, and polyamide 66 (PA66) was used as the matrix material of carbon fiber-reinforced PA66 (CFRPA66). The motion and interaction mechanism of PA66 and Al atoms under different temperatures and pressures during welding were studied. The results show that the changes of temperature and pressure during the welding process exert significant effects on the atomic diffusion and bonding behavior at the interface between PA66 and Al. When the reaction time is 10 ps, the absolute value of the interaction energy reaches the maximum value at 550 K or 1.5 MPa. The simulation results provide a theoretical basis for the optimization of welding process parameters between CFRPA66 and Al alloy, and lay a solid foundation for the industrial application of CFRTP/Al alloy composite joints.