The　specimen　is　assumed　to　be　a　rigid　mass　in　the　design　of　the　shaking　table　control　system　and　the　primary　frequency　of　the　specimen　is　about　8Hz.　However,　the　resonant　frequency　of　a　small-middle-sized　shaking　table　is　more　than　20Hz.　Therefore,　there　is　a　big　difference　between　the　specimen　and　the　shaking　table　system　caused　by　the　assumption　of　the　rigid　mass　for　the　specimen.　This　results　in　the　control　system　operating　in　a　narrow　frequency　band　and　poor　stability　reducing　the　replaying　precision　of　the　recorded　seismic　waves.　In　this　paper,　the　effects　on　the　controlling　performances　caused　by　the　quality,　frequency　and　damping　ratio　of　the　specimens　are　investigated　and　analyzed.　In　the　results,　the　replaying　precision　of　the　input　seismic　waves　which　the　frequency　is　near　the　one　of　the　specimen　are　poor,　some　of　the　inputs　are　amplified,　and　others　are　reduced.　The　maximum　value　is　amplified　more　than　3　times　compared　to　the　input　waves.　For　improving　the　above　disadvantages　caused　by　the　interaction　between　the　specimen　and　the　shaking　table,　the　real-time　compensation　of　reaction　algorithm　is　proposed　for　modifying　the　control　performance.　The　replaying　precision　of　the　input　seismic　records　is　greatly　improved　under　the　good　stability　of　the　control　system.