Manganese is a vital element in determining the mechanical properties of submerged arc welded metal. To ensure a reliable weld, the equilibrium model has been used for decades to predict and control the manganese content, particularly when MnO-bearing fluxes are applied. However, the equilibrium model only considers chemical interactions within the weld pool zone, leading to significant inaccuracies. To address this limitation, we propose a multi-zone model that accounts for all of the essential reaction zones in the submerged arc process via the Calphad technique. The model’s accuracy is verified by predicting the manganese content, the flux oxygen potential, and the neutral point location for the typical MnO-bearing fluxes covering acidic, neutral, and basic fluxes. The results indicate that the multi-zone model offers superior accuracy compared to the equilibrium model, which neglects significant oxygen improvement and alloy evaporation in the droplet zone. Further analysis of thermodynamic data reveals that the multi-zone model provides a more representative depiction of the variation trends in oxygen and manganese contents during the submerged arc welding process compared to the equilibrium model. Furthermore, this model can be utilized in the optimization of the submerged arc welding process, leading to improved quality and efficiency in heavy engineering industries. This study may provide an improved method for predicting the manganese content in welded C-Mn steel and deepen the understanding of manganese transfer mechanisms during the submerged arc welding process.