To shed light on the correlation effect between the capillary flow and phase transition of water in photothermal evaporation, the non-equilibrium molecular dynamics (NEMD) simulations were employed to investigate the evaporation of water in Multilayered graphene oxide membranes. It was initially found that water molecules need to overcome strong energy barriers to migrate upward by layers before evaporation, with the energy barrier increasing with the reduction in nanogap, hydroxyl content, or increase in layer spacing of graphene sheets. The strong energy barrier accordingly results in dramatic sensible heat conversion and high evaporation temperature. It was shown that the enhanced temperature and hydrophilicity both weaken the hydrogen bond strength of water molecules confined in 2-dimensional channels, contributing to the reduced evaporation enthalpy. The preferential pathways in graphene channels or the weakened hydrogen bonds in hydroxyl-functionalized graphene of water molecules were found to be important influences on capillary flow energy consumption, leading to differences in evaporation energy supply. In combination with these effects, the evaporation rate could be increased by up to 2 folds and an interfacial enthalpy of evaporation below 1500 kJ kg−1 could be achieved by properly tuning the configuration and chemical properties of the graphene membrane. Our findings lay a theoretical foundation for providing a strategy to improve the interfacial evaporation performance in desalination.