Abstract: Mega-sub structures based on the sub-structure isolation can solve the problem of height-width ratio limitation of the base isolated high-rise structures. The existing studies mostly focus on the theoretical and numerical analysis of the mega-sub structure under far-field ground motions. An experimental model of mega-sub structure was designed and manufactured, which had three mega floors. Lead rubber bearings were installed at the bottom of the sub-structure, then comparison shaking table tests of the uncontrolled and controlled mega-sub structure under near-field and far-field ground motions were performed. The results showed that setting isolation layer at the connection between the sub-structure and the main-structure had obvious damping effect of Tuned Mass Damper (TMD) on the main-structure's seismic responses and significant isolation effect on the sub-structure's seismic reactions. The seismic responses of the main-structure and the sub-structure under near-field ground motions are bigger than that under far-field ground motions. Under strong near-field ground motion, there is pounding between isolated sub-structures and main-structure, which has disadvantages towards structure's degree of comfort and safety.