Crosscover frequency response is produced by the rotor under abnormal vibration, so rotor jointly frequency fault sources cannot be satisfied statically independent request. The traditional source number estimation such as singular value decomposition method and standard independent standard analysis cannot extract fault sources. This paper estimates fault sources number with a non-negative method in the frequency domain, source and mixture system characteristics not in consider, and then to extract fault signals with wavelet packet, and separate recovered signals with small mutual information, to eliminate jointly frequency signal, to obtain independent non-correlated sources. The feasibility is verified by practical and theoretical methods.