Finite element method is powerful tool for predicting welding distortion. However, the mechanical phenomena in welding are strong non-linear transient problems and thermal-elastic-plastic FE analysis requires very long computational times. In this paper, based on the calculation of large-scale three-dimensional welding distortion problems, the limitation of the applicability of commercial software is discussed. Next, in order to accelerate the thermal-elastic-plastic FE program, the solver was changed into a sparse matrix iterative solver from a skyline solver. Further, an interactive substructure method is proposed as a method to reduce the computing time in three-dimensional welding distortion problems and its effectiveness is demonstrated. The effect which combined the interactive substructure method and the sparse matrix iterative solver was investigated.