The height of the F2 peak electron density (hmF2) is an essential parameter in studying ionospheric electrodynamics and high-frequency wireless communication. Based on ionosphere ray propagation theory, the physical relationship between M3000F2 and hmF2 is derived and visualized. Furthermore, based on the above physical theory and the machine learning method, this paper proposes a new model for determining hmF2 using propagation factor at a distance of 3000 km from the ionospheric F2 layer, time, and season. This proposed model is easy to understand and has the characteristics of clear principles, simple structure, and easy application. Furthermore, we used six stations in east Asia to verify this model and compare it with the other three models of the International Reference Ionosphere (IRI) model. The results show that the proposed model (PRO) has minor error and higher accuracy. Specifically the RMSE of the BSE, AMTB, SHU, and the PRO models were 20.35 km, 31.51 km, 13.59 km, and 5.68 km, respectively, and the RRMSE of the BSE, AMTB, SHU, and PRO models were 8.17%, 11.88%, 4.96%, and 2.12%, respectively. In addition, the experimental results show that the PRO model can better predict the trend of the hmF2 inflection point. This method can be further extended to add data sources and provide new ideas for studying the hmF2 over global regions.