The　three-dimensional　isolation　layer　is　moved　from　the　ground　to　the　bottom　of　the　sub-structures　in　mega-sub　structure　(megaframe-subframe　structure　system),　which　can　solve　the　problem　of　the　obvious　sway　reaction　of　the　3D　base　isolated　high-rise　structure,　and　the　structure　no　longer　subjects　to　the　constraint　of　height-width　ratio　limitation.　A　3-story　mega　frame　structure　model　is　designed　and　manufactured,　it　has　two　sub-structures　on　the　upper　structure　and　a　large　space　at　the　ground　floor.　4　3D　isolators　were　fixed　at　the　connection　of　the　every　sub-structure＇s　bottom　and　the　floor　of　mega-structure.　The　comparison　shaking　table　test　and　numerical　analysis　of　the　seismic　mega-sub　structure　and　the　3D　isolated　mega-sub　structure　under　rare　earthquake　excitation　of　horizontal　near-fault　and　far-fault　ground　motions　were　performed.　Results　indicate　that　moving　the　3D　isolation　layer　upward　does　not　prolong　the　structural　period.　The　vibration　control　effects　for　the　dynamic　responses　of　the　mega-structure　and　the　sub-structure　are　obvious,　and　they　are　seldom　influenced　by　the　type　of　the　ground　motion　and　site　type.　Due　to　the　pulse　effect　and　the　long-period　component　of　the　near-fault　ground　motions,　the　dynamic　responses　of　the　sub-structure　and　mega-structure　under　the　near-fault　earthquake　excitation　are　10%~20%　larger　than　that　under　the　far-fault　earthquake　excitation　of　the　same　site　type,　responses　under　the　near-fault　earthquake　excitation　of　site　type　are　10%~25%　larger　than　that　under　the　near-fault　earthquake　excitation　of　the　site　type　II.　©　2017,　Nanjing　Univ.　of　Aeronautics　an　Astronautics.　All　right　reserved.