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Dense non-rigid structure from motion (NRSfM) has long been a challenge in computer vision because of the vast number of feature points. As neural networks develop rapidly, a novel solution is emerging. However, existing methods ignore the significance of spatial–temporal data and the strong capacity of neural networks for learning. This study proposes a deep spatial–temporal NRSfM framework (DST-NRSfM) and introduces a weighted spatial constraint to further optimize the 3D reconstruction results. Layer normalization layers are applied in dense NRSfM tasks to stop gradient disappearance and hasten neural network convergence. Our DST-NRSfM framework outperforms both classical approaches and recent advancements. It achieves state-of-the-art performance across commonly used synthetic and real benchmark datasets.