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Aimed at composite fault of rotor misalignment and weak bearing fault,a fault diagnosis method based on Ensemble Empirical Mode Decomposition(EEMD) and Efficient Variant of FastICA(EFICA) is proposed.A single channel composite fault diagnosis signal is separated into multiple intrinsic mode functions(IMFs) with different feature by EEMD,which solve underdetermined problem in blind source separation(BSS).On the basis,EFICA can separate fault features that are needed from different IMFs.The results of simulation and rotor test stand experiment indicate that method can effectively separate fault features.