Laser transmission joining of dissimilar and biocompatible materials has potential applications in biomedical implants. In this work, a three-dimensional (3D) transient model for sequentially coupled thermal/mechanical analysis of laser transmission joining of 0.1mm thick PET film and 0.1mm stainless steel has been developed by using the ANSYS parametric design language APLD, along with a moving Gaussian laser heat source. It can be calculated how long it takes to reach the quasi-steady state through the stimulation of the temperature field. The calculated values of the joint width are in good agreement with the experimental results by comparison under conditions of different parameters, which indicates that the model is reliable and is helpful for optimizing process parameters. Then based on the temperature field, the residual stress field distribution on both PET and stainless steel surface is achieved by applying the indirect coupling methods to the analysis. this study also has laid a theoretical foundation for improving the stress distribution on the joint.