This paper presents an application of Hilbert-Huangtransform(HHT) analysis to health moni-toring for the Nanjing Yangtze River Bridge (NYRB), and a new method based on the empirical mode de-composition (EMD) to eliminate local strong disturbance from strain signals of main truss members of the NYRB. Firstly, measured vibration signals are decomposed into several intrinsic mode functions (IMFs) and a residue through EMD. Secondly, the signal amplitude and instantaneous frequency as a function of time, and frequency-time distribution of the amplitude designated as the Hilbert-Huang amplitude spectrum are ob-tained. Measured strain data of the NYRB with the disturbance of interphone are purified. Results of process-ing and analysis of measured signals of NYRB by using HHT as the train passing show the feasibility and va-lidity of the method in this paper. It also has demonstrated that the original data can be reconstructed with only four IMFs.