Based on the dynamic equations of underwater structures, the modal parameters under shock were identified with Hilbert-Huang Transform (HHT).The method combines the advantages of HHT for nonlinear and non-stationary signal, and the band-pass filters designed can select the cut-off frequency automatically, which can accurately obtain each modal response.Then, it can identify the structural natural frequencies and dampings with only one measured data in proper place.Finally, the accuracy and the validity of the method were verified on the basis of numerical simulation experiments, which identify the structural natural frequencies and dampings with one node response.It offers a practical method for the structural identification of modal parameters of underwater shock environment.