To solve the problem of SVP (Sound velocity profiles) representative error caused by the difficulty of obtaining continuous time series SVP in deep-sea operations, an SVP timing prediction method combining EMD (Empirical mode decomposition) and NARX (Nonlinear autoregressive neural network with external input) is proposed. To begin with, the time-series SVP are stratified according to different depths, and the time-series variation curves of sound velocity at different depths are obtained; Furthermore, the EMD is used to decompose the time series variation curve of sound velocity into multiple IMF (Intrinsic mode function) components, each component contains local characteristic signals of different time scales of the original signal. The NARX is used to establish a prediction model for each IMF components, and the prediction values of the sound velocity at different depths are obtained. The EMD-NARX, NARX and polynomial fitting model are analyzed and verified by Argo buoys data in the South China Sea, and the results of the experiment show that EMD-NARX improves the time series prediction accuracy of sound velocity by 32.24% and 65.15% compared with NARX and polynomial fitting, respectively, so EMD-NARX has a good prediction effect on the time series SVP of the deep sea.