To investigate the response characteristics of the rotor system in a high-temperature molten salt pump, a specific model of a cold salt pump was selected as the research object. The natural frequencies and mode shapes, critical speeds, and harmonic response analysis based on modal analysis of the rotor system with and without prestress were computed. The results indicate that with prestress, the natural frequencies of the rotor are higher compared to the rotor without prestress, and there is no clear pattern among the various vibration modes. The calculated critical speed for the second mode is much higher than the rotor’s operating speed. This suggests that the rotor system will not experience resonance at its operating speed, meeting design requirements and ensuring stable operation. When the rotor of the cold salt pump is subjected to unbalanced forces, vibrations occur in the x, y, and z directions. The region with the largest vibration amplitude is located at the fifth-stage impeller. At a frequency of 52 Hz, the corresponding harmonic response displacement reaches its maximum value, and this frequency remains unchanged with variations in the magnitude and position of the unbalanced force. Therefore, it is advisable to avoid operating the rotor system at the critical speeds corresponding to the first and second modes. Furthermore, the operating speed of the rotor system is much lower than the critical speeds corresponding to the first and second modes, so axial unbalanced forces generally do not affect the normal operation of the rotor system.