Accurate and reliable wave significant wave height(SWH) prediction is an important task for marine and engineering applications. This study aims to develop a new deep learning algorithm to accurately predict the SWH of deep and distant ocean. In this study, we combine two methods, Ensemble Empirical Mode Decomposition (EEMD) and Long Short-Term Memory (LSTM), to construct an EEMD-LSTM model, and explore the optimal parameters of the model through experiments. A total of 5328 hours of SWH data from November 30, 2020, to July 9, 2021, are used to train and test the model to predict the SWH for the future 1h, 3h, 6h, 12h, and 18h. The results show that the EEMD-LSTM model has the best results compared with other comparative models for short-term and medium- and long-term predictions. The RMSEs are 0.0204, 0.0279, 0.0452, 0.0941, and 0.1949 for the SWH prediction in the future 1, 3, 6, 12, and 18 h. It can be used as a rapid SWH prediction system to ensure navigation safety to a certain extent, which has great practical significance and application value.