Abstract: The flow-induced vibration is an important parameter to evaluate the operational stability of the pump turbine. In the present paper, based on the measured vibrational signal of the top cover of the pump turbine in China during the transient process of shutdown from the generating mode, the time-frequency analyses of the vibrational signal are carried out by adopting the empirical mode decomposition (EMD), the variational mode decomposition (VMD) and the Hilbert transform. The following conclusions are obtained. Firstly, compared with the EMD, the time-frequency information of the vibrational signal can be observed more intuitively from the Hilbert spectrum based on VMD. Then, the time-frequency analysis results show that the vibration of the top cover is mainly induced by the propagation of the abnormal pressure fluctuations caused by the rotor-stator interaction (RSI) between the rotational impeller and the stationary guide vanes within the flow passing components. Finally, with the gradual decrease of the discharge during the shutdown process of the unit, the abnormal pressure fluctuations excited by the fluids gradually weaken, leading to the gradual decreases of the intensity of RSI and the vibration of the top cover.