Theoretical　analyses　show　that　the　velocity　pulse　characteristics　of　ground　motions　adversely　affect　structural　responses　of　mega-sub　isolation　systems.　This　study　presents　an　extensive　shaking　table　test　conducted　to　investigate　the　seismic　responses　of　a　mega-sub　isolation　system　under　near-fault　ground　motions　with　velocity　pulses.　Two　steel　frames　were　used　as　test　specimens,　representing　aseismic　and　seismic　isolation　models.　Two　representative　groups　of　actual　ground　motion　records　with　velocity　pulse　characteristics　were　selected　as　inputs,　along　with　their　corresponding　synthetic　counterparts　with　the　same　acceleration　spectrum,　but　without　velocity　pulses.　Test　results　showed　that　near-fault　ground　motions　with　velocity　pulses　had　an　adverse　effect　on　the　seismic　responses　of　the　mega-sub　structure　system,　especially　on　the　displacement　of　the　isolation　layer　in　the　isolation　structure.　Compared　with　the　mega-sub　isolation　system,　more　nonlinear　behaviors　were　observed　in　the　aseismic　system.　Finite　element　analysis　of　the　mega-sub　aseismic　and　isolation　systems　was　conducted　by　using　SAP2000.　Satisfactory　agreement　was　observed　between　the　simulation　and　test　results,　and　the　differences　between　them　were　discussed　in　detail.　The　obtained　conclusions　can　provide　a　scientific　basis　and　valuable　reference　for　the　seismic　design　and　safety　evaluations　of　mega-sub　isolation　systems　under　near-fault　ground　motions　with　velocity　pulses.