Finite element (FE) simulation with inherent deformation is an ideal and practical computational approach for predicting welding stress and distortion in the production of complex aluminum alloy structures. In this study, based on the thermal elasto-plastic analysis, FE models of multi-pass butt welds and T-type fillet welds were investigated to obtain the inherent strain distribution in a 5A06 aluminum alloy cylindrical structure. The angular distortion of the T-type joint was used to investigate the corresponding inherent strain mechanism. Moreover, a custom-designed experimental system was applied to clarify the magnitude of inherent deformation. With the mechanism investigation of welding-induced buckling by FE analysis using inherent deformation, an application for predicting and mitigating the welding buckling in fabrication of complex aluminum alloy structure was developed.