According to the characteristic that Hilbert-Huang transform (HHT) can detect abnormity in signals, an HHT-based method to eliminate short-time strong disturbance was proposed. The signal with short-time strong disturbance was decomposed into a series of intrinsic mode functions (IMFs) and a residue by the empirical mode decomposition (EMD). The instantaneous amplitudes and frequencies of each IMF were calculated. And at abnormal section, instantaneous amplitudes and frequencies were fitted according to the data at normal section, replacing the fitted data for the original ones. A new set of IMFs was reconstructed by using the processed instantaneous amplitudes and frequencies. For the residue, abnormal fluctuations could be directly eliminated. And a new signal with the short-time strong disturbance eliminated was reconstructed by superposing all the new IMFs and the residue. The numerical simulation shows that there is a good correlation between the reconstructed signal and the undisturbed signal. The correlation coefficient is equal to 0.999 1. The processing results of the measured strain signal of a bridge with short-time strong disturbance verify the practicability of the method.