In this study, experiments and simulations were performed for fillet joint friction stir welding according to tool shape and welding conditions. Conventional butt friction stir welding has good weldability because heat is generated by friction with the bottom of the tool shoulder. However, in the case of fillet friction stir welding, the frictional heat is not sufficiently generated at the bottom of the tool shoulder due to the shape of the tool and the shape of the joint. Therefore, it is important to sufficiently generate frictional heat by slowing the welding speed as compared to butt welding. In this study, experiments and simulations were carried out on an aluminum battery housing made by friction stir welding an extruded material with a fillet joint. The temperature of the structure was measured using a thermocouple during welding, and the heat source was calculated through correlation analysis. Thermal elasto-plastic analysis of the structure was carried out using the calculated heat source and geometric boundary conditions. It is confirmed that the experimental results and the simulation results are well matched. Based on the results of the study, the deformation of the structure can be calculated through simulation even if the tool shape and welding process conditions change.