The relativistic magnetron with diffraction output (MDO) is promising to be the most compact narrow band high power microwave source. In this paper, based on the theory of S-parameters, a method named “choosing optimum” is proposed for the efficient design of the MDO in any wave band. By means of S-parameters, the π-TE31 mode conversion efficiencies of an S band MDO are calculated and then verified by three-dimensional particle-in-cell simulations. In order to illustrate the advantage of the choosing optimum method, the S-parameters of another L-band MDO are computed in a wide range of structure parameters and two results are chosen with detail information. Compared with the conventional method, the choosing optimum method is not only a shortcut, but also a convenient and easy way for choosing the high efficient MDOs in any wave band to meet the needs of different applications.