Base isolation is an effective means to reduce the seismic response of reactor plants. The isolation coefficient of the floor response spectra and the base isolator horizontal displacement are two critical performance objectives for assessing the isolation capability. These objectives are typically contradictory and cannot be optimized simultaneously. To adequately address the design demands of these performance objectives, the formulas relating the natural frequency of the base isolation system to the isolation coefficient of the floor response spectra and the displacement of the isolator are derived using the transfer function method based on the model of the single-degree-of-freedom (SDOF). Based on this derivation, a linear combination of the two performance objectives is utilized to construct an optimal design function. This leads to the development of a multi-objective optimization design method for base-isolated reactor plants, which is then applied to the numerical analysis and finite element simulation of the base-isolated Small Modular Thorium Molten Salt Reactor (SM-TMSR) plant. The results show that the isolation coefficients of floor response spectra and the horizontal displacements of base isolators obtained using the proposed optimized design method align closely with those from three-dimensional numerical simulations, indicating that the method is reasonable and feasible. Furthermore, the horizontal floor response spectra of the base-isolated SM-TMSR plant are significantly reduced compared to the non-isolated plant. The research in this paper provides valuable references for the base-isolated optimization design of SM-TMSR plant and related reactor plants.