A 3D thermal elastic-plastic finite element model was developed to predict welding residual stresses induced by full-penetration electron beam welding of Ti2AlNb alloy. Rotary-Gauss body heat source model was modified and improved to reflect the full-penetration weld. The results showed that the cross section profiles of the weld seam simulated with the modified heat source model agreed well with the experimental results. The residual stress distribution also had a good agreement between the numerical and experimental results, which proved the validity of the finite element model. The longitudinal tensile stresses played a major role in the welded joint of Ti2AlNb alloy and the region of residual stresses distribution was very narrow that extended a distance 3 mm away from the weld centerline. Compressive transverse stress was observed on the top and bottom surfaces while tensile transverse stress at the center of the weld, and the discrepancy was ascribed to the longitudinal and normal contracting of the weld. In addition, the phenomenon of local three dimensions residual tensile stresses appeared in the plate center.