Significant progress has been made over the last decades toward making active structural control, a viable technology for enhancing structural functionality and safety against natural hazards such as earthquakes and strong winds. In high performance active vibration control, it is required to establish an accurate model of the structure to avoid spillover instability of the control system. Moreover, due to the progress of the vibration control technology, it is necessary to identify not only the 1st but also the 2 nd and the 3rd vibration modes of the flexible structure. This paper presents the derivation method of modal parameters of flexible structures based on the system identification theory. In this identification, multi-decimation (MD) operation is applied to identify wide frequency region accurately. The advantages of this modeling method are as follows; (1) The vibrating time of the structure for identification is shorter than conventional sine-wave sweeping method. (2) The vibration modes that we focused on can be identified accurately. (3) By using circle curve fitting on each identified mode, one modal model applicable to multi-mode control can be derived as the system description. We apply the proposed identification method to the three-story structure, and construct the vibration control system based on the Hx control theory using the identified model. The effectiveness of the proposed identification and control methods is shown through the experimental analysis.