A new structural configuration that named Mega-sub controlled structure (MSCS) is presented in the process of tall buildings, super tall buildings and super tall tower construction. To further improve the structural control effectiveness of MSCS, new hybrid control method which employs active control and adjusts the stiffness of substructure is proposed. At the same time, the control law and dynamic equation are presented that assembling parameter matrixes for the MSCS subjected to horizontal seismic excitation. Then, the influence of adjusting structure parameter and active control parameter on control effectiveness, dynamic characteristic and control force of the MSCS under hybrid control is discussed. Results indicate that, the new hybrid control method proposed in the paper has the ability to develop a high level of response control effectiveness when subjected to seismic action, and a much better control effectiveness will be obtained after parameters optimization.