Due to low frequency resolution for closely spaced spectral components, i.e., the instantaneous frequencies (IFs) lie within an octave or even have intersections, the Hilbert–Huang transform (HHT) fails to separate such signals and consequently generates inaccurate time–frequency distribution (TFD). In this paper, a transform operator pair assisted HHT is proposed to improve the capability of the HHT to separate signals, especially those with IF intersections. The two operators of a pair are constructed to remove the chosen component that is clearly observed in the TFD of the signal, and then recover it from intrinsic mode functions (IMFs). With this approach, the components can be clearly separated and the intersections can also be identified in the TFD. Since a priori knowledge of the transform operator is usually not available in real applications, an iterative algorithm is presented to obtain a global transform operator. The effectiveness of the proposed algorithm is demonstrated by analysis of numerical signals and a real signal collected from a cracked rotor–bearing system during the start-up process. Moreover, the proposed approach is shown to be superior to the normalized Hilbert transform (NHT) as well as the ensemble empirical mode decomposition (EEMD).