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Accurate simulation of turbulent flows is fundamental to scientific and engineering applications. Direct numerical simulation (DNS) offers the highest fidelity but is computationally prohibitive, while existing data-driven alternatives struggle with stable long-horizon rollouts, physical consistency, and faithful simulation of small-scale structures. These challenges are particularly acute in three-dimensional (3D) settings, where the cubic growth of spatial degrees of freedom dramatically amplifies computational cost, memory demand, and the difficulty of capturing multi-scale interactions. To address these challenges, we propose a Physics-Enhanced Swin Transformer (PEST) for 3D turbulence simulation. PEST leverages a window-based self-attention mechanism to effectively model localized PDE interactions while maintaining computational efficiency. We introduce a frequency-domain adaptive loss that explicitly emphasizes small-scale structures, enabling more faithful simulation of high-frequency dynamics. To improve physical consistency, we incorporate Navier--Stokes residual constraints and divergence-free regularization directly into the learning objective. Extensive experiments on two representative turbulent flow configurations demonstrate that PEST achieves accurate, physically consistent, and stable autoregressive long-term simulations, outperforming existing data-driven baselines.