Two unbalanced signals with adjacent frequencies form beat signal in dual-rotor system with slightly different rotating speeds. The precision and timeliness of traditonal is not good. An improved Prony method is presented to extract frequecies of beat signal base on the decimation of bandpass filtered data, which can solve the problen that little rotation speed difference can not be measured easily. Least Square Method is used to extract magnitude and phase of beat signal with known frequencies, which can estimate accurately and quickly. In the end, simulation and analysis is given to prove correctness of the proposed method .