Various types of large substrate handling robots are used in the thin file solar cell manufacturing line as well as LCD or PDP production line. Because the robot handles the heavy substrate at high speed, there are some issues such as vibration control and the optimal design of arms and forks. As the substrate becomes larger and heavier, robot systems are also larger and the vibration issue of the robot end-effector becomes more important. In the paper, we established the robot modeling and the control architecture including the flexible part such as forks. Then, we performed dynamic simulation in the various condition and analyzed the characteristics of the fork vibration. We can reduce the vibration using the trajectory planning and input shaping algorithm and it was proved by experiment.