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Accurately, efficiently, and stably computing complex fluid flows and their evolution near solid boundaries over long horizons remains challenging. Conventional numerical solvers require fine grids and small time steps to resolve near-wall dynamics, resulting in high computational costs, while purely data-driven surrogate models accumulate rollout errors and lack robustness under extrapolative conditions. To address these issues, this study extends existing neural PDE solvers by developing a physics-integrated differentiable framework for long-horizon prediction of immersed-boundary flows. A key design aspect of the framework includes an important improvement, namely the structural integration of physical principles into an end-to-end differentiable architecture incorporating a PDE-based intermediate velocity module and a multi-direct forcing immersed boundary module, both adhering to the pressure-projection procedure for incompressible flow computation. The computationally expensive pressure projection step is substituted with a learned implicit correction using ConvResNet blocks to reduce cost, and a sub-iteration strategy is introduced to separate the embedded physics module's stability requirement from the surrogate model's time step, enabling stable coarse-grid autoregressive rollouts with large effective time increments. The framework uses only single-step supervision for training, eliminating long-horizon backpropagation and reducing training time to under one hour on a single GPU. Evaluations on benchmark cases of flow past a stationary cylinder and a rotationally oscillating cylinder at Re=100 show the proposed model consistently outperforms purely data-driven, physics-loss-constrained, and coarse-grid numerical baselines in flow-field fidelity and long-horizon stability, while achieving an approximately 200-fold inference speedup over the high-resolution solver.