The relationship between track vertical profile irregularity and vertical vibration acceleration of car body is analyzed by using Hilbert-Huang Transform (HHT). Firstly, actual measured vertical profile irregularity and vertical vibration acceleration of car body are decomposed by empirical mode decomposition (EMD) to obtain intrinsic mode function (IMF). Then, by comparing IMF waveform with the energy spectrum of the irregularity and vibration acceleration, the definitive correspondence of IMFs and adverse section of irregularity can be identified from vertical vibration acceleration of car body. Finally, regression analysis is taken for measured irregularities sample of track inspection car on Beijing-Guangzhou line. The quantitative relationship between track vertical profile irregularity and vertical vibration acceleration of car body is established with a wavelength between 1.5 m and 50m.