Abstract Evaporation through nanoporous membrane has attracted tremendous research attention as a ubiquitous natural phenomenon, which can be used in numerous applications. In this work, we explored the ultrathin water film evaporation process on nanoporous membrane based on non-equilibrium molecular dynamics simulation. A heat localization design of multilayer graphene coated at the bottom of membrane was implemented to reduce the heat loss along the non-evaporation direction. The underlying mechanism of water evaporation through nanoporous membrane was investigated after analysis of the average number of hydrogen bonds per water molecule, the temperature variation and the mean squared displacement of water molecular during the evaporation process. The results showed that the change of pore size will affect the water molecules structure. We also discussed the effect of heat localization design on ultrathin water film evaporation process. The result suggested that water molecules are more active and evaporation efficiency is improved correspondingly. This work reveals the feasibility of the novel nanoporous membrane structure design for enhancing heat and mass transfer, which can be adopted in efficient thermal management and low-cost approaches for water desalination.