A three-dimensional heat flux model for deep-penetrating electron beam welding (EBW) is established to mathematically describe the physical heat generation process during interaction between electrons and the dynamic molten pool free surface. Monte Carlo method is used to determine the electron-target interaction, and random distribution of initial electrons, progressive trajectory tracing and electron backscattering models are used to describe the spatial distribution of electrons absorption. The model is verified in preset keyholes and applied in the simulation on electron beam welding process, and the calculated bead shape shows a good consistency with experimental results.