Extracting the information of frequency-amplitude of the track irregularity through the Hilbert-Huang Transform（ HHT） spectrum,the clustering analysis is carried on the track irregularity HHT spectrum for the railways of same operating condition,then we can get the track irregularity marginal spectrum standard（ character） matrixes that are proper for describing different operation speed and the dynamic indexes,which will affect the security and comfort operation of the railway,based on these,the model of track irregularity HHT marginal spectrum-mahalanobis distance is built for the differentiate of running speed for the railway line and macroscopic predicting of the rail sections that would serious affect the railroad’s security and comfort operation.