The precise calculation of iron losses in permanent magnet synchronous motors (PMSMs) remains challenging due to the interplay between various disciplines such as electromagnetism, magnetism, and thermal/mechanical dynamics. Purely mechanistic models require detailed theoretical knowledge and exact parameters, often struggling to accurately describe complex systems, while purely data‐driven methods lack interpretability, which are susceptible to data noise and outliers in feature extraction and complicated pattern recognition. Consequently, this paper aims to present a hybrid mechanism‐data‐driven model for accurately estimating the iron loss for PMSMs, considering the multiphysics coupling effects. Specifically, based on the well‐defined physical principles, an advanced iron loss analytical model that simultaneously considers mechanical stress, temperature rise, harmonics, load currents, and changing frequency is developed and then utilised to calculate numerous loss data under different operating conditions, providing a certain level of stability and reliability for prediction accuracy. Subsequently, a convolutional neural network (CNN) algorithm is employed to perform deep learning to extract features and patterns from the data. By defining a suitable loss function, the pre‐trained model was fine‐tuned and optimised using a small amount of actual data. To validate its superiority, extensive numerical and experimental analyses are conducted on the prototype. The results demonstrate that the iron losses computed using this hybrid model overcome the limitations of singular methods by effectively leveraging both theoretical knowledge and real‐world data, thus accurately accommodating various application scenarios. This integrated approach enhances the accuracy, stability, and interpretability of the model, laying a solid foundation for more specialised applications in the future.