Accurate, simultaneous prediction of three-dimensional (3D) ocean temperature, salinity, and current fields is vital for understanding ocean dynamics and informing marine applications. This study introduces a Fourier Neural Operator (FNO)-based model specifically designed for this 3D multi-variable task, leveraging Fourier transforms to efficiently capture complex multi-scale spatio-temporal dependencies within the ocean state. Evaluated on multi-year data from the South China Sea, the FNO model demonstrates strong predictive skill. Compared against the Copernicus Marine Environment Monitoring Service (CMEMS) operational forecast product, our model achieved significant average reductions in Root Mean Square Error (RMSE) by 43.07 % and Mean Absolute Error (MAE) by 46.18 % (averaged across all four variables and the full 10-day forecast horizon). The FNO particularly excels in short-term predictions (1–3 days), outperforming conventional deep learning benchmarks (such as U-Net) in accuracy for key variables. Spectral analysis reveals this outperformance is linked to FNO's superior ability to represent the energy of multi-scale oceanic features, indicating a more faithful capture of their structures, while also offering substantial computational efficiency compared to traditional numerical simulations. While forecast accuracy decreases over longer periods, this work highlights the considerable potential of FNOs as a scalable and effective data-driven approach for advancing 3D oceanographic forecasting.
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