Nondestructive evaluation of three-dimensional welding residual stresses is demanded to predict crack propagation for observed cracks in in-service inspection. However, it is difficult to use neutron diffraction as on-site measurement technique because neutron diffraction is available just in special irradiation facilities. In the bead flush method, welding residual stresses for whole structure can be calculated from eigen-strains which are estimated by an inverse analysis from released strains due to removal of reinforcement of weld. Here, the removal of the excess metal is nondestructive treatment essentially. Although estimation accuracy of the bead flush method becomes poorer due to processing strains in the removal process, the method has been developed for considering the influence of processing strains by the first author. This study aims to demonstrate the effectiveness of this method for an actual welded joint. In this method, three-dimensional welding residual stresses can be estimated from measured strains by X-ray diffraction. Estimated results show that it is effective to estimate welding eigen-strains with gradient in the welding direction based on the response surface methodology. However, estimation accuracy of residual stresses has to be improved as a future work.