By means of the substructure approach in the frequency domain, equations of motion of the rubber - isolated structures are established considering the soil-structure dynamic interaction. The seismic responses of two shear-type base-isolated structures with an embedded rigid rectangular foundation are numerically simulated, and the influences of the different rigidities of soil on the effect of the base isolation and the seismic responses of the structure are investigated. It is concluded that rubber bearing isolation can reduce the dynamic characteristics of structures and reduce displacement of floor and basement relative to ground. Meanwhile, considering the dynamic soil-structure interaction may reduce the isolation effect of the rubber-isolated structures and the effect level is in direct proportion to the stiffness of the superstructure and inverse proportion to the stiffness of foundation soil.