The high-temperature molten salt pump is the core equipment in the small modular molten salt reactor with media temperatures up to 700 °C. The cantilever ratio of the molten salt pump is usually large. Excessively large cantilever ratios cause increased deformations and rotational amplitudes at the impeller, thus affecting the operational stability of the main pump; small cantilever ratios cause heavy temperature gradients, thus affecting the structural integrity evaluation. This paper used numerical simulation methods to calculate and analyze the temperature field, stress, and structural integrity, optimized the pump shaft cantilever length of the original scheme based on structural integrity using the dichotomy method, and analyzed the rotor dynamics of the optimization results. The results of this study show that the thermal expansion load caused by the temperature difference has a significant mechanical effect on the structure; the first-order critical speed of the rotor system of the optimized schemes has been improved, and the amplitude of the unbalanced response has been significantly reduced, which not only improves the operational stability of the rotor, also contributes to the compact design of the main pump of a small modular molten salt reactor.