To accurately predict the drying of a porous medium from saturated to unsaturated conditions over time, this paper proposes two-phase partitioning boundaries for liquid water evaporation and water vapor transport at the medium surface. A non-isothermal two-phase (liquid water and gas mixtures), two-component (dry air and water vapor) transport model with nonequilibrium and interface-dependent phase change is then developed. The governing equations are then numerical solved using COMSOL Multiphysics software and applied to describe a series of laboratory soil drying tests as examples. The performance of the proposed boundaries at the surface is illustrated by comparison with other three common used boundaries. The results show that a specific flux of vapor at the surface with a zero flux of liquid water cannot be adopted to describe the drying process of initially saturated media due to the lack of interconnected gas-filled pores. The merged liquid-vapor boundary applied in the Darcy–Richards model significantly prolongs the constant rate stage when the liquid water evaporation is dominant. Then, the effects of air/gas–water interfacial area and water retention parameters on the drying process are investigated. A faster reduction in the air–water relative interfacial area at the medium surface will shorten the drying process with earlier dominance of the vapor transport. An increased entry capillary pressure and a decreased pore size distribution index for the water retention curve will result in slower drying, more loss by vapor transport and a more homogeneous distribution of pore water respect to depth. The current study can promote the understanding of the evolution of drying mechanisms of a porous medium from saturated to unsaturated conditions.