In order to study the effect of interaction between soil and structure on the natural vibration characteristics of the structure, the calculation model of the soil - parallel foundation isolation system is established.,The ABAQUS software is used to establish the common structure and the parallel base isolation structure under different foundation conditions based on the principle of finite element method. The natural vibration frequency and the law of variation of the natural vibration period is discussed. The results show that the interaction between soil and structure on the natural vibration characteristics of the parallel base isolation structure is much smaller than that of the common structure,and the weaker the soil conditions of the site,the greater the degree of influence.