A method for flood discharge structure in the time domain is proposed in order to identify the operating modal parameters of high dams. First, useful information of the vibration signals is obtained by filtering the white noise and flow fluctuating noise using the wavelet threshold empirical mode decomposition filtering method. Then, the natural frequency and damping ratio of the system are identified using Hilbert-Huang transform (HHT). Finally, the modal orders and operating modal parameters of the flood discharge structure are determined using the singular entropy increment theory. Simulation results show that this method has strong robustness and superior precision, and can effectively avoid frequency confounding. Its successful use on the No.5 overflow section of the Three Gorges gravity dam provides the basis of the safe operation and online dynamic non-destruction monitoring of the high dam flood discharge structure.