In sampled-data positioning control systems, the vibrations caused by the mechanical resonances around a sampling frequency are not only the difficult to observe but readily excited by the control input in transient-state characteristics. To address this problem, we developed a control method that can suppress the zero-order-hold induced residual vibration in the sampled-data positioning control system. The study is on a shock response spectrum (SRS) analysis that handles the transient-state characteristics of mechanical resonances. The control method uses multi-rate notch filters that modify the acceleration input signals beyond the Nyquist frequency. We designed the notch filter based on the SRS analysis because the frequency response on the Bode diagram was not suitable for analyzing transient characteristics. The results of SRS analyses showed that the multi-rate notch filter was able to decrease the amplitude of residual vibrations caused by the mechanical resonances around the sampling frequency. To demonstrate the validity of the proposed method, simulations were conducted on a sampled-data positioning control system.