This paper focuses on viscous dampers disposition schemes regarding the vibration control of the Mega-Sub Controlled Structure System (MSCSS) subjected to rare earthquake excitation. It is intended in this study to evaluate the dynamic characteristics of the MSCSS compared with the traditional mega frame structure. The optimum arranging scheme matched with dynamic characteristics of MSCSS is given by analyzing the dynamic responses of the structure with different arrangements of viscous dampers on structure. Characteristics of hysteresis curve of viscous dampers in the optimum scheme are also investigated. Results shows that when dampers are installed in the two middle stories of the two sub-structures, the acceleration and displacement of MSCSS are well controlled compared to the conventional mega frame, reaching the optimum control effect. It is also shown that dampers are an indispensable component on MSCSS configuration. Reasonable arrangement of dampers on MSCSS can accurately contribute to improve structure seismic resistance. The efficiency of this structural system is fully presented through the optimum arrangement.