The geo-encased stone column is a new type of column which is wrapped with geosynthetics. Because the stone colume is encased by geosynthetic materials, its stiffness and shear strength is effectively improved. Thus far, however, limited research efforts have been devoted to the geo-encased stone column, especially in terms of aseismic behavior. In this study, shaking table tests on the composite foundations of geo-encased stone columns and stone columns were carried out to investigate the dynamic responses and aseismic behaviors of the two types of foundations. The acceleration, column-soil stress ratio, displacement of two composite foundations are monitored, and the failure phenomena were observed under the action of seismic waves of different types and amplitudes during the test. It is shown that the acceleration amplification factors in the horizontal direction at the top of the geo-encased stone columns and the soils between these columns are about two times that of the stone columns, and for the same saismic wave, the peak column-soil stress ratio of geo-encased columns is about three times that of stone columns. Compared with the stone column composite foundation, the geo-encased stone columns foundation forms narrower cracks in a larger area with the excitation of a 0.9g artificial seismic wave. The geogrid decreases the final settlement of the stone columns by 51%. It can be concluded that the geo-encased stone columns performs better than the stone columns during shaking.