Vibration-based diagnosis has been employed as a powerful tool in maintaining the operating efficiency and safety for large rotating machinery. However, the extraction of malfunction features is not accurate enough by using traditional vibration signal processing techniques, owing to their intrinsic shortcomings. In this paper, the relationship between effective eigenvalues and frequency components was investigated, and a new characteristic frequency separation method based on PCA (CFSM-PCA) was proposed. Certain feature frequency could be purified by reconstructing the specified eigenvalues. Furthermore, three significant perspectives were studied via the distribution of effective eigenvalues, and theoretical derivations were subsequently illustrated. More importantly, this proposed scheme could also be used to synthesize axis orbits of larger machines. Purified curves were so explicit and the CFSM-PCA exhibited higher efficiency than harmonic wavelet and wavelet packet.