Ocean forecasting is critical for various applications and is essential for understanding air–sea interactions, which contribute to mitigating the impacts of extreme events. While data-driven forecasting models have demonstrated considerable potential and speed, they often primarily focus on spatial variations while neglecting temporal dynamics. This paper presents the TSformer, a novel non-autoregressive spatio-temporal transformer designed for medium-range ocean eddy-resolving forecasting, enabling forecasts of up to 30 days in advance. We introduce an innovative hierarchical U-Net encoder–decoder architecture based on 3D Swin Transformer blocks, which extends the scope of local attention computation from spatial to spatio-temporal contexts to reduce accumulation errors. The TSformer is trained on 28 years of homogeneous, high-dimensional 3D ocean reanalysis datasets, supplemented by three 2D remote sensing datasets for surface forcing. Based on the near-real-time operational forecast results from 2023, comparative performance assessments against in situ profiles and satellite observation data indicate that the TSformer exhibits forecast performance comparable to leading numerical ocean forecasting models while being orders of magnitude faster. Unlike autoregressive models, the TSformer maintains 3D consistency in physical motion, ensuring long-term coherence and stability. Furthermore, the TSformer model, which incorporates surface auxiliary observational data, effectively simulates the vertical cooling and mixing effects induced by Super Typhoon Saola.