Condition monitoring and fault diagnosis via vibration signal processing play an important role to avoid serious accidents. Aiming at the complexity of multiple faults in a rotor-bearing system and drawback, the characteristic frequency of relevant fault could not be determined effectively with traditional method. The Spectral Kurtosis (SK) is useful for the bearing fault detection. Nevertheless, the simulation of experiment in this paper shows that the SK is unable to identify multi-fault of rotor-bearing system fully when different faults excite different resonance frequencies. A new multi-fault detection method based on EEMD and spectral kurtosis (SK) is proposed in order to overcoming the shortcoming. The proposed method is applied to multi-faults of rotor imbalance and faulty bearings. The superiority of the proposed method based on spectral kurtosis (SK) and EEMD is demonstrated in extracting fault characteristic information of rotating machinery.