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. However, in these methods, approximation error causes a high order vibration. On the other hand, methods based on distributed parameter model have low approximation error, but they needs a lot of calculation in time domain design. In this paper, to suppress vibration of resonant system, a novel position control system based on a transfer function of wave equation is proposed. Superposition of a traveling wave and the reflection wave cause ordinary wave and vibration occurs. From this viewpoint, the proposal is composed of two structure. First, a method of reflected wave rejection is proposed. When reflected wave is eliminated, vibration system is regarded as time delay system. Second, for suppression of vibration caused by time delay, wave compensator based on communication disturbance observer is proposed. In this paper, the proposed method is applied to a two-mass resonant system. The effectiveness of the proposed method is verified by experimental results.