The heat transfer behaviors are important to control the performance of Aluminum-Steel joint. However, because the models with weld tool are majorly tested for the same material joints, the heat transfer behaviors with weld tool for aluminum-steel joint are not fully understood. In this paper, a novel CFD model with weld tool is developed and tested to investigate the effects of weld tool on the aluminum-steel joint. The calculated temperature and thermal cycles for various traverse speed agreed well with the corresponding IR experimental results. It is found that the model with weld tool can decrease the temperature gradient and inhomogeneity of temperature field for aluminum-steel joint. The model with weld tool can provide calculated viscosity based on the validated temperature field to analysis the insufficient stirring defect of aluminum-steel joint.