Compound fault diagnosis is challenging due to the complexity, diversity and non-stationary characteristics of mechanical complex faults. In this paper, a novel compound fault separation method based on singular negentropy difference spectrum (SNDS) and integrated fast spectral correlation (IFSC) is proposed. Firstly, the original signal was de-noised by SNDS which improved the noise reduction effect of singular difference spectrum by introducing negative entropy. Secondly, the de-noised signal was analyzed by fast spectral correlation. Finally, IFSC took the fourth-order energy as the index to determine the resonance band and separate the fault features of different single fault. The proposed method is applied to analyze the simulated compound signals and the experimental vibration signals, the results show that the proposed method has excellent performance in the separation of rolling bearing composite faults.