This paper proposes a design method for the separation type 3D isolated structure, where the vertical isolation layer and the horizontal isolation layer are in separate arrangement in order that both layers are decoupling and the design calculation is more convenient and quicker. According to this method, a 2floor steel frame model is built as a 3D isolated structure. The simulated earthquake tests on the designed isolated model and a nonisolated structure model are then carried out by a shaking table. The experimental results shows that peak acceleration and floor shear of the separation type 3D isolated structure model are less than that of the nonisolated structure model. It is illustrated that the effect of the 3D isolation is good.