Inverse analysis method based on the elastic finite element method is a newly approach to estimate the inherent deformations in typical welded joints. However, when this approach is employed to obtain the inherent deformations, the 3-D coordinates before and after welding at a limited number of locations in the welded joints should be known. In order to improve the precision of inverse analysis results, a new algorithm is proposed to obtain the 3-D coordinates at the limited locations on neural plane of weldment by using a contact 3-D measurement system. In addition, two bead-on plate welded joints with 2 mm and 3 mm thickness are selected as research objectives to demonstrate the effectiveness of the new method. The calculated 3-D coordinates are used as known parameters and inherent deformation components are gained based on inverse analysis method, then deformations of the two thin-plate bead-on joints are predicted by the use of inherent strain method. The comparison shows that there are big differences between the two joints with different thickness. The proposed measurement method and algorithm can accurately obtain the 3-D coordinates on the neural plane and the inherent deformation components obtained by inverse analysis method are accurate and effective.