Abstract: The increasing frequency ratio of a super-sub structure has a great influence on aseismic performance of the substructure of the isolated masonry with an added storey. The Root-Mean-Square (RMS) ratio of the substructure response in an isolation structure and a no-isolation one is developed by random vibration theory. The variation law of the RMS ratio of the substructure acceleration with the different frequency ratios is analyzed. The results show the isolated structure has a good aseismic performance before it damaged. But the seismic response of substructure is increased with the stiffness degeneration. The acceleration response of the isolated structure can exceed the no-isolated structure. A shaking table test for an isolated structure with added storey and a no-isolated structure with an added storey was carried out. The variation of damping effect was analyzed by the comparison with the floors acceleration responses between sound and damaged structure. The experiment shows that the acceleration responses of an initial isolated model were smaller than that of a no-isolated model. But the damping effect of the isolated structure was reduced with the damage of the substructure and the acceleration responses were even exaggerated. The results show a good agreement with theoretical conclusions. The negative influence of the damaged substructure must be considered in the design for the isolated structure with an added storey.