Abstract: In order to study the optimal parameters of the isolation layer in mega-sub control system,equation of motion of mega-sub control system was established,and the parameter optimization of megasub control system was studied based on the genetic algorithm theory where base shear was used as the optimization object function.The sensitivity of the stochastic response of the mega-sub control system to the structure's parameters was analyzed by virtual excitation method and perturbation method.From the sensitivity of variance of the main structure story drift,isolation layer story drift,and the absolute acceleration variance of the top substructure to each parameter.It shows that the sensitivity of the response of the structure is weaker to the stiffness of substructure,and is more sensitive to the quality of substructure.The stiffness and damping of isolation layers,which also explains the reasons why that the mass ratio,frequency ratio and damping ratio are usually used for performance analysis of mega-sub control system.