Rotor Complex Fault Vibration signals are very hard to analysis since there are many frequencies lies in them. It needs new signal processing methods to deal with these problems. Empirical Mode Decomposition (EMD) is a non-stationary signal processing method developed recently. The frequency heterodyne EMD method can improve the frequency resolution of EMD by shifting the original frequencies to enlarge the frequencies ratio between components. It proves that the method can enhance the performance of EMD easily and effectively. The paper discusses the principle and steps of this method in detail and uses it to analyse rotor complex fault signals. The result shows that frequency heterodyne EMD method can separate different faults and detect the weaker faults in complex fault more effectively than that of normal EMD method.