The roll eccentricity signal is complex and high frequency periodic signal which is mixed with all kinds of random disturbances. Because of the limitation of the FFT method to signal analysis, a new method which is the combination of the RootMultiple Signal Classification (RootMUSIC) and the Prony method is presented. The frequency and the number of eccentricity harmonics are estimated by the RootMUSIC method, and simultaneously the amplitude and phase of eccentricity harmonics are estimated by the Prony method. The simulation results show that in the case of low SNR (Signal Noise Ratio), the frequency, amplitude, and phase of eccentricity harmonics can still be estimated. It is superior to FFT in frequency resolution and noise rejection.