The new staggered story isolated system is developed according to the base isolated system and the mid-story isolated system. Non-linear finite element model of an eighteen stories new staggered story isolated structure is established. For a comparative analysis, the models of a base isolated structure, a mid-story isolated structure, and an aseismic structure are also established, and their shock absorption performances and damages are analyzed for comparison. The results indicate that the new staggered story isolated structure has a small seismic response, good shock absorption performance which is feasible for application. Besides, the shock absorption performance of the new staggered story isolated structure is a little worse than the base isolated structure but slightly better than the mid-story isolated structure. The bottom of core tube and the story below the frame isolated story have large acceleration response which needs to be paid more attention in design.