As an effective way of passive damping, isolation technology has been widely used in all types of building structures. Currently, for its theoretical analysis, it usually follows the rigid foundation assumption and ignores soil-structure interaction, which results in calculation results distortion in conducting seismic response analysis. In this paper, three-dimensional finite element method is used to establish finite element analysis model of large chassis single-tower base isolation structure which considers and do not consider soil-structure interaction. The calculation results show that: after considering soil-structure interaction, the dynamic characteristics of the isolation structure, and seismic response are subject to varying degrees of impact.