An on-line method based on robust mu analysis is presented to evaluate the stability margin of multi-loop aeroservoelastic system from flight testing data. The flight data is preprocessed to remove noise by wavelet filter in time-frequency domain. The method for stability analysis is described and the classical stability margin used for single-input-single-output (SISO) system has been extended to multi-loop system. With the present definition for uncertainty, the guaranteed bounds on gain and phase margin can been calculated for a specified mu value. A nonparametric identification is applied to determine the open-loop transfer function from testing data. This method enables us to implement on-line stability evaluation without theory model. Finally, the analysis results are compared with return difference matrix method to illustrate the efficiency of the new method