Combined with wavelet threshold denoising and Ensemble Empirical Mode Decomposition (EEMD) decomposition, an identification method based on Manta Ray Foraging Optimization-BP (MRFO-BP) neural network for vibration signals of residual pressure utilization hydraulic units is proposed to distinguish the vibration signal of each unit. The feature vectors of vibration signals are extracted by wavelet denoising and EEMD decomposition. The weights and thresholds in BP neural network are optimized by the MRFO algorithm. The feature vectors are input into the optimized BP neural network to realize the identification and classification of vibration signals. Compared with Particle Swarm Optimization-BP (PSO-BP) neural network, Bat Algorithm-BP (BA-BP) neural network, and BP neural network, the results show that the identification rate of each measuring point from the MRFO-BP neural network is greatly improved. The average identification rate of other measuring points is 98.514%, except the identification rate of the generator, which is 85.389%. Therefore, the MRFO-BP neural network has better stability and higher identification accuracy and can identify and classify vibration signals more accurately. The conclusions can provide theoretical basis for vibration signals identification of residual pressure utilization hydraulic unit. When the vibration signal of each unit cannot be clearly distinguished, the vibration signals of the units are identified by the method proposed in this paper. According to the obtained results, a feasible classification method can be provided for the vibration signals belonging to different units.