Abstract: Based on the model of Penzien, the calculation model of isolated structure in consideration of pile-soil interaction (SSI) is established, the vibration equation is derived, and the effect of interaction of pile-soil on isolation structure is analyzed. At the same time, the effect of earthquake inputted from free ground or end of pile on isolated structure is compared. The conclusions suggest that the interaction of pile-soil has some effect on isolation structure, which is much more smaller than that on non-isolated structure. For this reason, the SSI can be ignored in the design of isolation structure.