Abstract: Shaking table test of the mega-sub control system was carried out in order to study the seismic performance of this system. Test specimens were 3 steel frames, called aseismic model, isolated model and isolated-bottom consolidated model, respectively. Nonlinear dynamic time analyses of the test models were performed using SAP2000. Theoretical results were compared with the experimental results on some structural responses including the acceleration response and story drift response of the mega-structure, the story drift response of the substructure, and the deformation of the isolation layer. The results shows that theoretical analysis are in good agreement with the experimental results. The structural responses of the isolated model and isolated-bottom consolidated model are greatly reduced compared with that of the aseismic model, which can be illustrated by both the theoretical results and experimental results. It is concluded that the isolation devices can reduce the structural responses effectively, and make the structure safer than that without isolation devices.