Reduction of microvibration is regarded as important in high-technology facilities with high precision equipments. In this paper, smart control technology is used to improve the microvibration control performance. Mr damper is used to make a smart base isolation system amd fuzzy logic control algorithm is employed to appropriately control the MR damper. In order to develop optimal fuzzy control algorithm, a multi-objective genetic algorithm is used in this study. As an excitation, a train-induced ground acceleration is used for time history analysis and three-story example building structure is employed. Microvibration control performance of passive and smart base isolation systems have been investigated in this study. Numerical simulation results show that the multi-objective genetic algorithm can provide optimal fuzzy logic controllers for smart base isolation system and the smart control system can effectively reduce microvibration of a high-technology facility subjected to train-induced excitation.