Though input shaping technologies are used to reduce residual vibration of flexible systems, most input shaping technologies adopt open-loop control scheme and can not handle the uncertainties such as non-zero initial conditions, external disturbances, model parameter variations and system nonlinearities. A closed-loop input shaping control scheme, which combines an input shaper with a vibration damper, is proposed for suppressing the residual oscillations of the multi-mode flexible systems. The input shaper prevents the operator from inadvertently adding energy to the system through the commands, and the vibration damper acts as energy damper to remove the energy that has entered into the system from aforementioned uncertainties, so the two controllers cooperate with each other to suppress the residual vibration. Compared with the open-loop input shaper, the robustness and disturbance resistance of the closed-loop input shaper is strengthened. The proposed control technology is used in crane experiment to suppress the residual oscillation of payload.