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.　©　2017,　Editorial　Department　of　Journal　of　Hunan　University.　All　right　reserved.