The magnetorheological (MR) fluid damper-based semiactive control systems have received considerable attention for protecting structures against natural hazards such as strong earthquakes and high winds. In this paper, a novel modal controller using wavelet packet transform (WPT) is proposed for the vibration control of distributed structures. In the proposed control system, the WPT method is utilized to decompose the acceleration measurement and select the modes containing most of the WPT energy component as the dominant modes. Then, a modal controller is designed to control the dominant modes and the optimal active control force is solved. Finally, Clipped-optimal con- trol law is adopted to determine the voltage applied to each MR damper. A Kalman-filter observer, which estimates the full controlled modal states from local accelerometer feedbacks, is designed for rendering the controller to be more applicable to distributed structures with a large number of degrees of freedom. A numerical example of a stadium roof structure installed with MRF-04K damper is presented. The effectiveness of the controller is evaluated under both Tianjin and El Centro earthquake excitations. The superior performance and adaptability of the controller for versatile loading conditions are demonstrated through the comparison with traditional truncated modal controller.