This study investigates the thermo-mechanical behavior and residual stress characteristics of friction stir welding (FSW) in an aluminum inverter housing using finite element analysis (FEA). FSW experiments were first conducted under various tool rotation and traverse speed conditions, and temperature histories were measured using K-type thermocouples. The optimal process condition was identified through tensile testing, and the heat input was estimated by comparing experimental and numerical results. The estimated heat source was incorporated into a transient thermal elasto-plastic analysis to evaluate deformation and residual stresses in an inverter housing model. The results indicated that residual stress distributions varied depending on the welding start position. In particular, when welding started at P3 (near thick ribs and bosses) residual stresses were reduced by approximately 30% compared to P1, owing to the higher local stiffness and enhanced heat dissipation that mitigated temperature gradients. Conversely, welding initiated at P1, a flat region with insufficient reinforcement, resulted in higher stress concentrations. These findings confirm that the welding start position significantly influences residual stress behavior in inverter housings and provide fundamental insights for developing residual stress control strategies in FSW of large-scale components.