Neural Network (NN) technology is revolutionizing the modeling paradigm in the engineering arena, enhancing simultaneously model precision and process speed. Nevertheless, the deficiency of physical interpretability in current NN models causes an unattainable demand for the quantity of training data, especially when dealing with high-dimension physical behaviours. In this work, a Hierarchical Physics-Informed Neural Network (HPINN) framework is proposed to address the 3D magnetic modeling issue of Medium Frequency Transformers (MFTs). By establishing the knowledge transfer channel between the cross section and the equivalent space, the inferior 2D model parameter search space, which is restricted by Dowell’s equation and accessible 2D magnetic data information, can be mapped into the superior 3D search space. Accordingly, with limited 3D training data, the performance of the HPINN framework is still guaranteed around the optimal state. The structural embedding of physics knowledge reduces the model's reliance on 3D training data, thereby relieving the strict computing requirement at the data generation stage. Finally, according to the training results and experiment verifications, with only one-third computational burden used in the classic NN model, the average error of this proposed HPINN framework is reduced to 1%, and the maximum error does not exceed 10%.