A dual-stage control system design method is presented for the three-axis-rotational maneuver and vibration stabilization of a spacecraft with flexible appendages embedded with piezoceramics as sensor and actuator. In this design approach, the attitude control and the vibration suppression sub-systems are designed separately using the lower order model. The design of attitude controller is based on the variable structure control (VSC) theory leading to a discontinuous control law. This controller accomplishes asymptotic attitude maneuvering in the closed-loop system and is insensitive to the interaction of elastic modes and uncertainty in the system. To actively suppress the flexible vibrations, the modal velocity feedback control method is presented by using piezoelectric materials as additional sensor and actuator bonded on the surface of the flexible appendages. In addition, a special configuration of actuators for three-axis attitude control is also investigated: the pitch attitude controlled by a momentum wheel, and the roll/yaw control achieved by on-off thrusters, which is modulated by pulse width pulse frequency modulation technique to construct the proper control torque history. Numerical simulations performed show that the rotational maneuver and vibration suppression are accomplished in spite of the presence of disturbance torque and parameter uncertainty.