A mathematical model based on the cellular automaton−finite element (CAFE) method was developed to study the solidification structure evolution of DD98M superalloy ingots during electron beam smelting (EBS). The model couples heat transfer, fluid flow, and solute diffusion. Grain nucleation and growth occur in the direction opposite to the heat flow. The simulation results show good agreement with experimental observations. The influence of the nucleation parameters on the solidification structure was systematically examined. The results indicate that increasing the maximum bulk nucleation density leads to a reduction in grain size and promotes the formation of a larger equiaxed grain region, while simultaneously reducing the extent of the columnar grain region. In contrast, increasing the mean bulk nucleation undercooling results in a smaller equiaxed region and an expanded columnar grain zone. The standard deviation of bulk nucleation undercooling is found to have a negligible effect on grain morphology.