With the rapid development of the society, there are more and more high-rise buildings in the city, among which the structure of large-chassis single-tower buildings is complex, and there is a lateral stiffness mutation at the transition storey between the large-chassis and superstructure, which is prone to structural damage under the action of earthquakes. Therefore, the seismic design of large-chassis single-tower structure and its corresponding seismic isolation technology research have attracted much attention. In this paper, the large-chassis single-tower building as the research object, the numerical models of its correspondent seismic structure and inter-storey isolation structure were established by Structure Analysis Program 2000 (SAP2000), and the different horizontal stiffness of seismic isolators for inter-storey isolation structure were considered. The dynamic responses of interlaminar shear force, floor acceleration and storey drift of the above two structures under the action of fortification and rare earthquakes were numerically simulated and compared to explore the influence of the horizontal stiffness of seismic isolators on the isolation performance of the large-chassis single-tower structure with inter-storey isolation, which provides a reference for the inter-storey isolation design of the large-chassis single-tower structure. The research results show that with the increase of the horizontal stiffness of seismic isolators, the storey drift and interlaminar shear force increase, and the storey drift of the substructure increases more significantly when the inter-storey isolation storey is set between the large-chassis and the tower. Therefore, it is recommended to adopt the seismic isolators with good flexibility and large ultimate horizontal displacement when designing inter-storey isolation for large-chassis single-tower structure.