Adaptive disturbance rejection filter (ADRF) approach, an active vibration control for flexible spacecraft, is developed and its parameters are identified using a closed-loop system method. Particularly, semi-physical experimental study of a maneuvering spacecraft equipped with a flexible manipulator is implemented to demonstrate the improvement of the attitude control performance. The control system consists of two main parts: (1) optimal input shaper is applied to the flexible manipulator to suppress the vibration and alleviate the effect of the vibration on the spacecraft; (2) ADRF is presented to mitigate the equivalent periodic disturbance caused by the nonlinear coupling between the spacecraft motion and the manipulator vibration. The disturbance frequency adaptation tracks the frequency of the periodic disturbance using adaptive notch filter, and the obtained frequency is then fed to disturbance rejection filter. The ADRF approach can provide optimal sets of gains based on the characteristics of the system. The semi-physical experimental results show that the frequency tracking method works quite well to be used in a real-time controller. The results also indicate that the ADRF can provide significant vibration reduction and improve the attitude control accuracy of the spacecraft body.