Abstract: With a thin plate lap joint as the research object, a three-dimensional finite element model with the thermal elastic-plastic method, and a two-dimensional shell finite element model with the temperature load method were established. The welding deformation simulation of the thin plate lap joint was carried out with the two-dimensional shell model by changing the element connection mode of lap joint area (shell element, CE element, CP displacement coupling and beam element), and the best element connection mode was determined. The two-dimensional shell model with optimized element connection mode was modified by the inherent strain obtained by the three-dimensional model. The modified two-dimensional shell model was used to predict and verify the welding deformation, and compared with the three-dimensional model. The relationship between the mesh size and the inherent strain near the weld seam was analyzed. The results show that CP displacement coupling connection was the best element connection mode. The relative errors between the maximum angular deformations on the side edges of the upper and lower base metals (parallel to the welding direction, at 125 mm and 62.5 mm from the center of weld seam) simulated by the two-dimensional shell model with optimized element connection mode and test results were 1.73% and 2.81%, respectively, indicating the model had high accuracy in predicting welding deformation. Compared with the three-dimensional finite element model, the numbers of meshes and the calculation time of the two-dimensional shell finite element model were reduced by more than 90%, and the calculation accuracy was equivalent to that of the three-dimensional model. The verification coefficient of the inherent strain was inversely proportional to the 1.085th power of the mesh size near the weld seam. When the mesh size near the weld seam was 15 mm, the maximum relative error of the angular deformation obtained by simulation was only 6.67%.