Friction stir welding (FSW) is a solid-state jointing technology, and has the advantages of high joint strength, low residual stress, and small deformation after welding. During FSW, the welding temperature directly influences the quality of the weldment. A heat generation model of FSW medium thickness aluminum alloy 2219 is established considering the friction heat generated at the interface between the tool and the workpiece and the plastic deformation heat of the weldment material near the tool. The heat transfer model is set considering heat conduction, convection, and radiation. Using JMatPro technology, temperature-related material parameters of aluminum alloy 2219 are obtained. The built heat generation model is imported into the simulation software ABAQUS through the DFLUX subroutine, and the simulation of FSW process is achieved. The effectiveness of the simulation is verified by FSW experiments. The simulation has high prediction accuracy. Based on the simulation, the influence of welding parameters on temperature distribution is explored; subsequently the influence of welding temperature on mechanical properties of welded joint is also studied. The research guides the prediction of the temperature distribution and the improvement of the mechanical performance of FSW medium thickness aluminum alloy 2219.