A new vibration signal denoising method of hydropower unit based on noise-assisted multivariate empirical mode decomposition (NA-MEMD) and approximate entropy is proposed. Firstly, the NA-MEMD is used to decompose the signal into a number of intrinsic mode functions. Then, the approximate entropy of each component is computed. According to a preset threshold of approximate entropy, these components are reconstructed to denoise vibration signal of hydropower unit. The analysis results of simulation signal and real-world signal show that the proposed method is adaptive and has a good denoising performance. It is very suitable for online denoising of hydropower unit's vibration signal.