Significant Wave Height (SWH) is a crucial parameter in ocean wave dynamics, impacting coastal safety, maritime transportation, and meteorological research. Building upon the TimesNet neural network, a recent advancement in the realm of time series prediction in deep learning, this study proposes an integrated approach combining Empirical Mode Decomposition (EMD) with TimesNet, introducing the EMD-TimesNet model for SWH forecasting. The TimesNet model’s multidimensional spatial mapping guarantees effective historical information extraction, while the EMD approach makes it easier to decompose subsequence characteristics inside the original SWH data. The predicted Root Mean Square Error (RMSE) and Correlation Coefficient (CC) values of the EMD-TimesNet model are 0.0494 m and 0.9936; 0.0982 m and 0.9747; and 0.1573 m and 0.9352 at 1 h, 3 h, and 6 h, respectively. The results indicate that the EMD-TimesNet model outperforms existing models, including the TimesNet, Autoformer, Transformer, and CNN-BiLSTM-Attention models, both in terms of overall evaluation metrics and prediction performance for diverse sea states. This integrated model represents a promising advancement in enhancing the accuracy of SWH predictions.