The construction of pure niobium superconducting radiofrequency (SRF) cavities requires the use of electron beam welding (EBW), particularly the welding in the equatorial region. The prediction of residual stress and welding distortion with high precision is important for the design of welding tooling and the optimization of welding parameters due to the detrimental influence that welding deformation and residual stress have on the performance of the SRF cavities. However, the EBW of the equator region is carried out with beam oscillation, a suitable simulation approach for the mechanical analysis of oscillating EBW received less attention. In this study, a novel heat source with two reverse 2D Gaussian heat source was created for the finite element method (FEM) simulation of EBW with beam oscillation. Additionally, a computational fluid dynamics (CFD) simulation of the molten pool was run as a guide for adjusting the parameters of the designed heat source. The FEM simulation with 2D Gaussian heat source was taken as a comparison. An EBW experiment of niobium sheets was performed for the validation of weld width, residual stress and welding distortion. The simulated molten pool of this model has a wider width, which is considerably closer to the actual measurement, and the thermal results reveal a smoother temperature gradient in the joint simulated with the proposed heat source. The mechanical results demonstrate that the estimation of the residual stress distribution and welding contradiction by the designed model are likewise more in accordance with the outcomes of the experiment. In the future, the oscillating EBW of sheet metal made of additional materials will be simulated using the suggested method.