This paper proposes the real-time hybrid shaking table testing methods to simulate the dynamic behavior of a soil-structure interaction system with dynamic soil stiffness by using only a structure model as the physical specimen and verifies their effectiveness for experimental implementation. Experimental methodologies proposed in this paper adopt such a way that absolute accelerations measured from the superstructure and shaking table are feedback to the shaking table controller, and then the shaking table is driven by the calculated motion of the absolute acceleration (acceleration feedback method) or the absolute velocity (velocity feedback method) of foundation that is required to simulate the dynamic behavior of a whole soil-structure interaction system. The shaking table test is implemented by reflecting the dynamic soil stiffness, which are differently approximated from the theoretical one depending on the feedback methods, on the shaking table controller to calculate soil part. The effectiveness of the proposed experimental methods is verified by comparing the response measured from the test on a foundation-fixed structural model and that obtained from the experiment of a soil-interaction system under the consideration in this paper and by matching the dynamic soil stiffness reflected on the shaking table controller with that identified using the experimentally measured data.