In order to solve the fault transient signal extracting and analysis problem in aircraft power system, Hilbert-Huang Transform (HHT) is used in this paper. The complicated signal can be decomposed into a finite Intrinsic Mode Functions (IMF) by the Empirical Mode Decomposition (EMD), which makes the instantaneous frequency meaningful. Thus, the fault transient signal can be analyzed by instantaneous frequency and Hilbert marginal spectrum. The results show that HHT can analyze the fault signal from time and frequency domains, detect fault time, extract and analyze harmonic components from the fault signal for the aircraft power system. It is demonstrated by actual analysis that HHT is one effective way for analysis of the fault signal in the aircraft power system.