In order to accurately identify the damage of hydraulic structure, a valid damage diagnosis method combining variational mode decomposition(VMD) and Hilbert-Huang transform (HHT) marginal spectrum is proposed. Firstly,a kind of combined wavelet threshold and empirical mode decomposition (EMD) method is used to filter out the noises, which can reduce the disturbance of environmental noise to structural damage characteristic information. Then variance dedication rate method is used to realize the dynamic fusion of multi-point vibration signals, extracting the vibration characteristic information of the overall structure accurately and comprehensively. Finally, VMD method is used to decompose the fused signals into many of intrinsic mode function(IMF) components, and then Hilbert transform is applied to each IMF to obtain the marginal spectrum of fused signals. In the proposed method, the damage sensitive index is defined based on VMD marginal spectrum and served as the damage feature vector of hydraulic structure, combining the damage sensitive index and Mahalanobis distance function to identify the damage of hydraulic structure. The proposed method is applied to study the vibration responses of cantilever beam model. The results show that the proposed method can effectively extract the damage characteristics and identify the operation conditions of hydraulic structure, which provides a basis for the safe operation of hydraulic structure.