In the actual working process, the source of vibration signal is not only the rotor itself, so the detected vibration signal will become complicated. This complex signal makes it difficult to accurately measure the existence of crack. In this paper, a novel method, which includes complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) and continuous wavelet transform (CWT), is proposed to analyze the cracked rotor-rolling bearing system. The CEEMDAN-CWT successfully separates the vibration signal of the rotor itself from the original signal and provides results similar to the simulation signal. At the speed below 2000 rpm, the 2X frequency difference between cracked rotor and healthy rotor in CEEMDAN-CWT spectrum is about 1, while the difference of FFT spectrum of original signal is about 0.6, which shows the superiority of the novel method in extracting rotor vibration signals from complex vibration signals.