The　equations　of　motion　of　a　mega-sub　structure　control　system　are　established　in　this　paper.　The　control　mechanism　of　the　system　is　obtained　based　on　the　analysis　of　its　dynamic　characteristics.　The　analysis　results　show　that　with　increase　of　the　substructure　mass,　the　working　mechanisms　are　changed　from　a　tuned　mass　damper　mechanism　to　a　seismic　isolation　mechanism.　Parametric　optimization　of　the　mega-sub　structure　control　system　is　studied　based　on　the　genetic　algorithm　and　complex　modal　theory,　in　which　the　base　shear　is　used　as　the　objective　function.　By　using　Hilbert-Huang　transform,　the　marginal　spectrum　of　the　mega-sub　structure　control　system　is　obtained.　Numerical　simulation　indicates　that　the　marginal　spectrum　intensity　of　the　top　displacement　and　acceleration　are　reduced　significantly　for　both　the　primary　structure　and　sub-structure,　compared　to　the　traditional　mega-sub　structure　system.　Finally,　time　history　analyses　of　the　mega-sub　structure　control　system　show　that　the　input　energy,　dissipated　energy　and　deformation　energy　in　the　mega-sub　structure　control　system　are　greatly　reduced　in　compared　with　the　traditional　mega-sub　structure　system.