To address the misidentification problem of signals containing unknown faults for hydropower units, a progressive fault diagnosis system is designed. Firstly, in view of the non-stationary and nonlinear vibration signals of hydropower units, the method of complementary ensemble empirical mode decomposition is used to process the normal and fault vibration signal samples, and the intrinsic mode function (IMF) and residual components with different frequencies are obtained. Then the IMF energy moment is calculated and used as the feature vector. Furthermore, a classifier (IMF-K1) is constructed based on the feature vector samples of the normal vibration signals of hydropower units, fault symptom indicators, and K-means algorithm to determine whether the hydropower unit is faulty; a classifier (IMF-K2) is constructed based on the feature vector samples of the fault vibration signals of hydropower units, fault symptom indicators, and K-means algorithm to determine whether the hydropower unit has the known fault; a classifier (IMF-bidirectional long short-term memory neural network (BiLSTMNN)) is constructed to distinguish the fault type of hydropower units by combining the eigenvector samples of known fault vibration signals, fault symptom indicators, and BiLSTMNN. Finally, a progressive fault diagnosis system for hydropower units is constructed using IMF-K1, IMF-K2, and IMF-BiLSTMNN, and comparative experiments are designed using the sample data from the rotor test bench and actual hydropower unit. The results show that the designed progressive fault diagnosis system has greater effectiveness in mining signal features and high fault diagnosis accuracy.