In order to effectively remove noise from the signal, a denoising method for submarine cable vibration signals based on variational mode decomposition (VMD) and permutation entropy (PE) is proposed. This method first uses VMD to decompose the signal into several intrinsic mode functions from high frequency to low frequency, and then calculates the PE values of each mode component to quantitatively characterize its degree of randomness. Next, wavelet thresholding is applied to the intrinsic mode function (IMF) components with more noisy information, and the denoised submarine cable vibration signal is obtained through signal reconstruction. In order to verify the effectiveness of this method, a simulation experimental system for monitoring the vibration signals of submarine cables based on Brillouin optical time-domain analysis(BOTDA) is established. The vibration signals of submarine cables under three working conditions of erosion, friction, and anchoring are obtained through experiments.The experimental results show that the proposed method can effectively remove high-frequency noise in submarine cable vibration signals. The signal-to-noise ratios of the three types of signals, namely erosion, friction, and anchoring, are increased to 30.257 8 dB, 29.635 4 dB, and 38.786 2 dB, respectively, with a low standard deviation.