Semi-active control of base-isolated structures using magneto-rheological (MR) dampers is well studied in recent years. However, there is a study gap for sensitivity and reliability analyses assessment of the structure in the literature. Besides, the reliability analysis of the structures based on the importance of the building from a user perspective categorized into three groups including very high, high, and medium is an interesting topic that is considered in this study. Extension of the study for the case of uncontrolled base-isolated structures and controlled ones in both passive-off and passive-on modes of the MR dampers and tuning the command voltage of the MR dampers by a multi-objective modified clipped optimal (MOMCO) controller are also addressed in this paper in different seismic hazard regions with different peak ground accelerations (PGAs). The Monte Carlo simulation (MCS)-based Sobol's indices and importance sampling (IS) method are applied for the sensitivity and reliability analyses, respectively. Studies are conducted on an 8-story nonlinear base-isolated structure. The sensitivity analyses show the main seismic responses are more influenced by the changing uncertainties of the stochastic ground acceleration; the mass, and stiffness of the structural model; and the yield force of the isolation system. MR dampers can significantly reduce the failure probabilities of the structures in different seismic hazard regions. By increasing seismic hazard, an increment is observed in failure probability. Enhancing the importance of the building from medium to very-high status leads to an increase in the failure probabilities of the structure in all cases. However, the performance of three control cases in reducing the failure probabilities of the structure is often increased. The MOMCO controller and passive-on mode represent fewer failure probabilities than the uncontrolled and passive-off mode in different seismic hazard regions and groups. However, the MOMCO gives the best performance in the reduction of failure probabilities.