The evaporation duct is a special atmospheric stratification that significantly influences the propagation path of electromagnetic waves at sea, and hence, it is crucial for the stability of the radio communication systems. Affected by physical parameters that are not universal, traditional evaporation duct theoretical models often have limited accuracy and poor generalization ability, e.g., the remote sensing method is limited by the inversion algorithm. The accuracy, generalization ability and scientific interpretability of the existing pure data-driven evaporation duct height prediction models still need to be improved. To address these issues, in this paper, we use the voyage observation data and propose the physically constrained LightGBM evaporation duct height prediction model (LGB-PHY). The proposed model integrates the Babin–Young–Carton (BYC) physical model into a custom loss function. Compared with the eXtreme Gradient Boosting (XGB) model, the LGB-PHY based on a 5-day voyage data set of the South China Sea provides significant improvement where the RMSE index is reduced by 68%, while the SCC index is improved by 6.5%. We further carried out a cross-comparison experiment of regional generalization and show that in the sea area with high latitude and strong adaptability of the BYC model, the LGB-PHY model has a stronger regional generalization performance than that of the XGB model.