Hamiltonian learning (HL), enabling precise estimation of system parameters and underlying dynamics, plays a critical role in characterizing quantum systems. However, conventional HL methods face challenges in noise robustness and resource efficiency, especially under limited measurements. In this work, we present , an approach that incorporates the Schrödinger equation as a soft constraint via a loss function penalty into the ML procedure. This formulation allows the model to integrate both observational data and known physical laws to infer Hamiltonian parameters with greater accuracy and resource efficiency. We benchmark iPINN-HL against a deep-neural-network-based quantum state tomography method (denoted as DNN-HL) and demonstrate its effectiveness across several different scenarios, including one-dimensional spin chains, cross-resonance gate calibration, crosstalk identification, and real-time compensation to parameter drift. Our results show that iPINN-HL can approach the Heisenberg limit and exhibits robustness to noises, while outperforming DNN-HL in accuracy and resource efficiency. Therefore, iPINN-HL is a powerful and flexible framework for quantum system characterization for practical tasks.

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