To solve the problem of seldom use of isolation technology in super high-rise buildings as well as the restriction on the tensile capacity of isolation bearing and structural height-width ratio limitation，in this paper，the combined isolation layers consisting of lead rubber bearings and elastic sliding bearings were set at the bottom of the sub-structures in the new mega-sub structure system. An experimental model of mega-sub structure was designed and manufactured，which included three mega floors. Shaking table tests of the uncontrolled and controlled mega-sub structure under near-fault and far-fault ground motions were carried out. Vibration control effects of combined isolation layers on the seismic vibrations of main-structure and sub-structures and the influences of near-fault ground motions were studied. The results show that the combined isolation layer at the bottom of sub-structure is equivalent to a tuned mass damper for the main-structure，and it has obvious damping effect of TMD on the seismic reactions of main structure，while it is equal to a base isolation structure for the sub-structure itself，and it has significant isolation effect on the seismic responses of sub-structure. Seismic reactions of the main-structure and the sub-structures under near-fault ground motions are larger than that under far-fault ground motions due to the pulse effect.