In order to accurately identify the dynamic response of bridges caused by vehicle passage, a bridge structural dynamic parameter identification method is proposed by combining the variational mode decomposition (VMD) method and Hilbert-Huang transform (HHT) marginal spectrum with permutation entropy. Firstly, the original vibration signal is decomposed by VMD to obtain the multiple Intrinsic Mode Function (IMF) components. And then the permutation entropy of each IMF component is calculated. The IMF component with the lower permutation entropy is selected by using the characteristic that the more stable the signal is, the smaller the permutation entropy is. Finally, the HHT transformation is performed to obtain the marginal spectra of each IMF component. Compared with the calculation results of an example through simulation, the result shows that the method can effectively identify the dynamic response of the bridge caused by vehicle passage and also adapt to the lower vertical frequency of the bridge. The vertical frequency of the bridge under vehicle excitation is accurately extracted. The factors of vehicle speed, pavement roughness and vehicle weight have little effect on the calculation results of VMD-HHT marginal spectra. The results may provide a reference for the safe operation and health status evaluation of bridge structures.