The describing function method is employed for the nonlinear control analysis and design of a flexible spacecraft equipped with pulse modulated reaction jets. The method provides a means of characterizing the pulse modulator in terms of its gain and phase for structural mode limit cycle analysis. Although the describing function method is inherently inexact and is not widely used in practice, a new way of utilizing it for practical control design problems is presented. It is shown that the approximations inherent in the method can be accounted as a modeling uncertainty for the nonlinear control robustness analysis. The pulse modulated control system of the Intelsat 5 spacecraft is used as an example to illustrate the concept and methodology developed in the paper. The nonlinear stability margins predicted by the describing function analysis are verified from nonlinear simulations.