Reverse dual-rotation friction stir welding (RDR-FSW) is a novel variant of conventional FSW process. The key feature is that the tool pin and the assisted shoulder rotate reversely and independently during the process; thus, it has great potential to improve the weld quality and lower the welding loads through adjusting the rotating speeds of the tool pin and the assisted shoulder independently. In this study, a 3D model of RDR-FSW process is developed to conduct the numerical simulation of heat generation, material flow, and temperature profile during the process. Heat generated due to plastic deformation and friction at the tool-workpiece contact interfaces are both considered. Streamlines show that there are two material flows with reverse direction, which is beneficial to the uniformity of both the temperature and the microstructure at the advancing side and retreating side. The simulation results show that rotating speeds of the assisted shoulder and the tool pin have great effects on the shape and size of the thermo-mechanically affected zone (TMAZ). The calculated peak temperatures at typical locations match with the experimentally measured ones. It lays solid foundation to optimize the process parameters in RDR-FSW.