In this study, the deformation of friction stir welding on the aluminum battery housing material(AL6063-T5) applied to the electric vehicle was effectively predicted through experiments and numerical simulations. The temperature data were measured during the friction stir welding experiment, and the numerical simulation was carried out using the experimental temperature data. In the heat transfer analysis, the temperature distribution of the structure over time was calculated using the Reynolds equation. The final friction stir welding deformation was calculated by performing the structural analysis using the calculated temperature distribution data over time. The thermal elasto-plastic analysis was performed according to the friction stir welding process conditions and the welding sequences. Finally, the optimum welding condition was derived that the welding speed is 1000 mm/min and the rotation speed of the tool is 2000 RPM.