The traditional passive base isolation is the most widely used method in the engineering practice for structural control, however, it has the shortcoming that the optimal control frequency band is significantly limited and narrow. For the seismic isolation system designed specifically for large earthquakes, the structural acceleration response may be enlarged under small earthquakes. If the design requirements under small earthquakes are satisfied, the deformation in the isolation layer may become too large to be accepted. Occasionally, it may be destroyed under large earthquakes. In the isolation control system combined with rubber bearing and magnetorheological (MR) damper, the MR damper can provide instantaneous variable damping force to effectively control the structural response at different input magnitudes. In this paper, the control effect of semi-active control and quasi-passive control for the isolation control system is verified by the shaking table test. In regard to semi-active control, the linear quadratic regulator (LQR) classical linear optimal control algorithm by continuous control and switch control strategies are used to control the structural vibration response. Numerical simulation analysis and shaking table test results indicate that isolation control system can effectively overcome the shortcoming due to narrow optimum control band of the passive isolation system, and thus to provide optimal control for different seismic excitations in a wider frequency range. It shows that, even under super large earthquakes, the structure still exhibits the ability to maintain overall stability performance.