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Motion control of flexible arms is more difficult than that of rigid arms, however utilizing its dynamics enables improved performance such as a fast motion in short operation time. This paper investigates a ball throwing robot with one rigid link and one flexible link. This robot throws a ball at a set speed with a proper control torque. A mathematical model of this ball throwing robot is derived through Hamilton’s principle. Several patterns of torque input are designed and tested through the proposed simulation models. The parameters of each torque input pattern is optimized and determined by chaos embedded vector evaluated particle swarm optimization (CEVEPSO). Then, the residual vibration of the manipulator after throwing is suppressed with input shaping technique. Finally, a real experiment is set up for the model checking.