An efficient and reliable numerical analysis for three-dimensional (3D) multipass welding simulation is proposed in this paper. A fast analysis method to calculate 3D residual stress distribution in the multipass welds using the iterative substructure method (ISM) was developed and validated using other numerical analysis and measurement results. First, the analysis results by the developed method were compared with those by a conventional method using a commercial finite element analysis code. The comparisons were made for the analysis accuracy and the computational speed of the residual stress analysis in a multipass welded pipe joint. Both sets of analysis results for residual stress agreed well with each other. Furthermore, it was clarified that the developed analysis method could calculate the residual stress in a shorter computing time than the conventional analysis method. Next, the residual stress of the pipe joint computed by the developed analysis method was compared with measurement results obtained using the strain gauge method, and the good analysis accuracy was shown. Consequently, these comparisons demonstrated that the developed method for multipass welding simulation based on the ISM could calculate the residual stress distribution much faster at high analysis accuracy even when the size of the welding problems, such as for multipass welding, was large.