In this work, based upon molecular dynamics (MD) simulations, two kinds of nanopores with different pore sizes and functional groups were constructed to study the directional transport of water molecules. The results showed that the functional groups at the edges of pores had a significant effect on water flux, and graphene oxide (GO) nanopores modified by COH (hydroxyl) and CH (hydrogen) had good water permeability. However, for small pore sizes, the flux from hydrophilic GO-COH was smaller than that from hydrophobic GO-CH. For large pore sizes, the hydrophilic functional group's water flux was nearly 24 % higher than that of the hydrophobic functional group. Due to the solid molecular affinity between water and GO-COO− surface, the water flux of GO-COO− was much higher than that of GO-COOH. The GO-COO− hole showed selective penetration of water. This research proves that the hydrophilic COO− on GO sheet can improve the permeability of water molecules, whereas the water flux is about 19.5 % higher than that of GO-COOH. As a desalination membrane, the water flux of the GO membrane designed in this paper is 3–4 orders of magnitude higher than that of the existing commercial reverse osmosis membranes.