Electron beam melting has become a key technology for the preparation of superalloy ingots, and its solidification structure directly affects the casting quality as well as the performance of subsequent billet forging. It is practical and important to carry out a systematic and detailed analysis of the structure formation during the solidification of the ingot. Considering the high cost and difficulty of experimental research, a mathematical model of the filling and solidification process of superalloy preparation was established via ProCAST software to predict the evolution of the temperature field, flow field, and solidification structure during the layer-by-layer filling and solidification process under the conditions of electron beam melting. This paper simulated the temperature field, flow field, and solidification microstructure of a casting superalloy ingot with a diameter of 220 mm under different pouring speeds (0.5, 1.0, 1.5, 2.0, and 4.0 kg/s). It then explored the change rules of the temperature field, flow velocity, and solidification structure in relation to the pouring speed. The results show that during the layer casting process of nickel-based superalloy  ingots, the temperature at the top of the ingot is high, whereas the temperature at the bottom is low, which results in sequential solidification from the bottom to the top. As the pouring speed increases, the temperature gradient increases significantly, and the influence of the upper layer alloy melt on the temperature change in the lower layer alloy decreases; that is, the temperature rise decreases. In the center region, heat accumulation is more significant, which may lead to greater thermal stresses and defects inside the ingot. Changes in the pouring speed have a greater influence on the maximum speed of melt flow and melt level fluctuations. With increasing pouring speed, the fluid velocity change at the monitoring points clearly fluctuates, especially in the area near the pouring inlet. The greater the pouring speed is, the greater the impact depth of the alloy liquid. The pouring speed significantly affects the grain growth behavior and orientation distribution during solidification. A lower pouring speed is conducive to the formation of columnar crystals with larger grain sizes and more ordered orientations, whereas a higher pouring speed promotes grain refinement of the center region and more disordered grain orientations.