This study aims to determine the optimal parameters for the electron beam melting process by employing a modified transient three-dimensional thermal model. The validity of the thermal model is confirmed through experimental results. Moreover, the proposed method establishes mathematical relationships between the resulting molten pool temperature and process parameters. A broader range of process parameters for a new Ni–Co-based superalloy was achieved by investigating the effects of scanning velocities (10–100 mm/s), scanning radius (20–60 mm), and melting mass (1500–3100 g) on temperature at various electron beam power levels (10–30 kW). Regression models were established between scanning velocities-temperature, and scanning radius-temperature under different electron beam power levels. These models laid the foundation for real-time automatic control of molten pool temperature. Significantly, orthogonal experimental design and response surface method are employed to conduct a multi-objective optimization based on sixteen experiments and three parameters. The results of multi-objective optimization indicate that with a smelting mass of 1.5 kg, an electron beam power of 11 kW, a scanning radius of 60 mm, and a scanning velocity of 75 mm/s, the energy consumption is 34.95 kW h, and the theoretical mass loss of Ni element is 0.002 kg. The desirability is 91.2 %.