Vibration control of resonant system is an important problem in industry applications. The reason is that degradation of task accuracy and destruction of materials are caused by vibration. Under such a background, state feedback control, H ∞ control, and resonant ratio control based on lumped parameter system have been researched for vibration suppression of system with flexible mechanism. On the other hand, methods in distributed parameter model need a lot of calculation in time domain design. In this paper, to suppress vibration of resonant system, a novel position controller based on a transfer function of wave equation is proposed. Superposition of a traveling wave and the reflection wave causes ordinary wave and vibration occurs. Therefore, a method of reflected wave rejection is proposed. Moreover, the proposed method is applied to a two-mass resonant system and three-mass resonant system. Because the proposed method is based on a distributed parameter model, all vibration modes can be suppressed. The effectiveness of the proposed method is verified by experimental results in a 2-mass and 3-mass resonant system.