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Precision of positioning and operation are enormously affected by vibration while flexible manipulator is running. Great attention has been paid on the research on vibration control of flexible manipulator. However, there is shortage of effective and uniform real-time simulation platform to date. Based on the study of coupled modeling and dynamic characteristics, the two-link flexible manipulator system made of piezoelectric smart structure was established. The manipulator's motion was controlled by single-chip computer system and serial communication module provided by simulink. The date exchange between manipulator system and the MATLAB workspace was implemented by the data acquisition module, which combined physical system with virtual environment. So the real-time simulation system for vibration control of flexible manipulator was set up. Adopted the PID control algorithm, the entire experimental system was debugged. The results showed that the system can work normally, and the PID control algorithm can also effectively suppress the vibration of flexible manipulator. The platform can be used for vibration control experimental research and the actual system.