In this paper, a novel method of numerical computation of the natural frequencies, depending on the most important running parameters for an ultrasonic motor, is described. The analyzed configuration by the Space Division of Alenia Spazio, Rome, within an Italian Space Agency (ASI) development program, is the flexural traveling wave one. The dynamic equations for the stator and the rotors of the ultrasonic motor are assumed into a differential system, whose equations are coupled by terms that represent interface generalized forces. In order to calculate natural frequencies of the motor-coupled terms of the equations are worked out with respect to the variables of the degrees of freedom. Hence, the mass, damping, and stiffness matrix for the whole system are obtained, then resonance frequencies, depending on the most important running parameters such as axial preload of the motor, are calculated. The results are compared with numerical ones, obtained by a finite element modeling (FEM) model, showing a good agreement.