Laser Transmission Joining (LTJ), which is a joining process of polymers by using different transmission rates of materials, was studied numerically. Unlike previous studies, energy loss by reflection at the surface was included. Besides, energy absorbed in the transparent substrate is also considered to increase the accuracy of the analytical results. Furthermore, thermal deformations of the substrates were also calculated. Temperature distribution of the substrates on the joining process could be effectively predicted by using the thermal analysis model developed, which could also analyze the rising phenomenon of the absorbing substrate by bulge effect. Calculated results show that temperature of the absorbing substrate is higher than that of transparent substrate when the laser is being radiated, and this temperature difference causes more thermal deformation in absorbing substrate, which results in the surface rise of the absorbing substrate. Comparison of calculated results with corresponding experimental results could confirm the validity of the numerical analysis model proposed.