The present study investigated the influence of temperature on molecular interdiffusion at the interface during the laser transmission welding of 3D-printed continuous carbon-fiber-reinforced thermoplastic composites. In order to accurately measure the temperature at the weld interface, a series of thermocouples were embedded in the laser-absorbent composite part. Two different molecular interdiffusion models were implemented to calculate the degree of healing and to predict the effects of temperature on the welding process. The degree of healing and the weld line width were computed and compared with microscopy observations. The discrepancy between the two proposed numerical models was less than 6%. Both models showed good agreement with the experimental data, with an average error of 13.28% and 7.26%, respectively. The results revealed a significant correlation between the thermal history and molecular interdiffusion at the interface. Furthermore, the relationship between the welding parameters (laser beam scanning speed) and weld line width was established. The findings of this study provide a comprehensive understanding of the underlying mechanisms involved in the laser welding of 3D-printed composites and offer insights to optimize the welding process for enhanced weld quality and superior mechanical properties in the final product.