For a flexible manipulator system, the unwanted vibrations deteriorate usually the performance of the system due to the coupling of large overall motion and elastic vibration. This paper focuses on the active vibration control of a two-link flexible manipulator with piezoelectric materials. The multi flexible body dynamics (MFBD) model of the two-link flexible manipulator attached with piezoelectric sensors and actuators is established firstly. Based on the absolute nodal coordinate formulation (ANCF), the motion equations of the manipulator system are derived and motion process and dynamic responses of the system are simulated. According to the time varying feature of system, a fuzzy PID controller is developed to depress the vibration. This controller can tune control gains online accommodating to the variation of the system. Control results obtained by the fuzzy PID control and the conventional PID control indicate that the fuzzy PID controller can effectively suppress the elastic vibration of the manipulator system and performs better than the conventional PID controller.