Authors proposed a new method to evaluate both welding deformations and residual stresses based on the eigen-strain methodology, which is applicable to the finite element (FEM) analysis. In the proposed method, three-dimensional eigen-strains are estimated by the inverse analysis using the Truncated Singular Value Decomposition (TSVD) method and the penalty method. Numerical simulations are carried out for a butt-welded plate with larger angular deformation in the thickness direction. As a result, eigen-strains to express both welding deformations and residual stresses with higher accuracy could be estimated successfully.