The elastic deformations and residual vibrations in flexible mechanisms are raised along with the motions of rigid bodies in light-duty and high-speed mechanisms. The motions of flexible bodies couple with the motions of rigid bodies that result in lower locating precision of the mechanism. In this paper, based on researching the dynamical performances of the flexible mechanisms with a rigid mode, time-delay is introduced in a control system and PD combined with input-shaping control is presented for the mechanical structures. The dynamical behavior of PD combined with input-shaping control system, subject to step inputs, is investigated. The actuator efforts and energy usage of PD combined with input-shaping control system are described in general formula. Given the condition of the same feedback gains as the PD feedback control, the PD combined with input shaping control minimizes actuator effort by 56%, saves energy by 47%, and speeds system response.