As the environmental pollution issue has recently become significant, environmental regulations in Europe and the United States are being strengthened. Thus, there is a demand for the quality improvement of emission after-treatment systems to satisfy the strengthened environmental regulations. Reducing the amount of welding heat distortion by optimization of the welding order of each part could be a solution for quality improvement since the emission after-treatment system consists of many parts and each assembly is produced by welding individual ones. In this research, a method to derive a welding sequence that effectively minimizes welding deformation was proposed. A two-stage simulation was performed to obtain the optimal welding sequence. In the first stage, the welding sequence was derived by analyzing the number of welding groups in each assembly of a structure. The derived welding sequence was verified by performing a thermal elasto-plastic analysis and comparing it with the experimental results.