The positioning and operating precision of flexible manipulator is reduced by vibration in the process of running, and vibration suppression is different when the flexible manipulator is controlled by different control algorithms. According to the two-link rigid-flexible-electric coupling piezoelectricity flexible manipulator, the active vibration control method of flexible manipulator was proposed based on the fuzzy self-tuning PID algorithm. The effective fuzzy rules were established With MATLAB fuzzy control toolbox. The design and simulation of fuzzy control system whose PID parameters was self-tuning online was realized. The conventional PID control algorithm was also compared. The simulation and experimental results showed that this two algorithms could suppress vibration of flexible manipulator, but the fuzzy self-tuning PID controller had the advantages of fast response, stronger robustness and easy adjustment, and it was better to improve the dynamic performance of control system.