Structural reaction analysis under frequent earthquake and rare earthquake was carried out using time- history method. Every single-tower structure was chosen as an analysis modal, which can reflect real structural reaction. The results show that seismic response decreases obviously and story shear force and overturning moment are far less than that of aseismic structures. Horizontal reduction coefficient is lower under rare earthquake. Story drift is mainly centralized at isolator layer, which approaches zero on superstructure. The isolated structure shows whole translational motion. Reduction degree of seismic response for the three towers is more or less from each other.