In the long-term service period, many factors may lead to serious damages and deficiencies to the structure, such as complicated working conditions, inadequate investigation and design, poor management, aging of structure, etc. Therefore, it's very important to study the online monitoring method for flood discharge. According to the special advantages of HHT in instantaneous characteristics analysis and signal processing, an online monitoring method for flood discharge structure damage based on HHT is put forward in this paper. Firstly, after obtaining the HHT energy spectrum of measured responses, the energy distribution vector, defined as ηi , can be calculated. Then, because of the η i differences between undamaged and damaged situations, we determine the structure anomaly indexes and the warning threshold. Finally, having been calculating the anomaly indexes of adjacent time periods, the damage online monitoring can be realized. The results from the numerical simulation test of a guide wall demonstrate that the anomaly indexes mentioned above can accurately identify the structure damage and have anti-noise ability to some degree. However, the further research for estimating the damage location and degree need to be developed in the next period.