The Disturbance observer (DOB) method is known to be effective in enhancing the performance of dynamic systems in the presence of disturbances. DOBs of various structures have been proposed to improve systems’ sensitivity functions for better disturbance rejection performance and robustness. However, the improvement to the sensitivity function may deteriorate robustness and transient responses. In this paper, we propose a new systematic method of designing the DOB. This method is based on the robust stabilization of the normalized coprime factor plant description and H∞ loop shaping method. In our method, good system robustness can be achieved by Nehari stability margin, and the design parameters of the Q-filter for system robustness and performance can be determined systematically using a target loop transfer function. We applied this method to a MEMS stage. Simulation results show that the disturbance effect of the stage is reduced, and a robust system is achieved in the presence of parameter uncertainties.