Based on the shaking table test for the base isolated structure built on the soft interlayer ground and rigid foundation, a 3-D finite element model is established to simulate the dynamic soil-structure interaction, which has the same size with the test system. Then, the natural frequencies of the isolated structure and the acceleration responses of the soil-structure interaction system are compared and analyzed. As results, the experimental results given by the shaking table test are mostly consistent qualitatively, such as the natural frequency of isolated structure, the acceleration response of isolation layer, the earthquake responses of model foundation, and so on. However, the results by two different methods have obviously difference in numerical value, thus it is proved that the shaking table test can be used to simulate the earthquake responses of the dynamic soil-structure interaction qualitatively but not quantitatively.