Aiming at the problem that the impact signal of ship propulsion shafting early rubbing fault has strong periodicity and is easily submerged by strong background noise, a method for identifying the characteristic fault information of the shafting based on the structural vibration of the hull is proposed, which is called EEAF (mean: EEMD + Autocorrelation Analysis + FFT). Firstly, Ensemble Empirical Mode Decomposition (EEMD) is performed on the collected complex hull structure vibration signal to obtain a series of inherent mode components (IMF). Then, guided by the nature of autocorrelation function, screening out the IMF component of the periodic component; Finally, the fast Fourier transform is performed on the corresponding decomposition layer, and the spectrum analysis is used to identify the feature quantity of the early rubbing fault of the shafting. The effectiveness and feasibility of the proposed method are verified by the simulation of the shafting fault and the actual ship test.