The laser welding process is employed for sealing the metal bipolar plate of fuel cells. The targets for this method are stamped thin plates, no more than 0.1 mm in thickness. In the welding process, it is necessary to accurately control the depth of fusion to make it in a semi-penetration state. A heat source model that can accurately simulate the physical properties of welding is needed to quantitatively study the small-scale precision welding process by numerical simulation. In this paper, a modification was made to the existing laser welding heat source model to create a heat source model suitable for semi-penetration laser welding, with a focus on penetration control. By applying single factor analysis, the effect trend of each variable within the heat source model on heat flux output was determined. Through the welding experiment, the welding parameters and the weld cross-section shape of the small deformation bipolar plate are obtained. The trial-and-error method is used to adjust the value of each variable in the heat source model. The welding process is simulated by using the heat source model with the well-modulated parameters, and the simulation results are consistent with the real semi-penetration state. Consequently, this heat source model holds potential as a reference model for future numerical quantitative investigations in bipolar plate welding.