In this work, molecular dynamics simulations were employed to study the permeation of ethanol-water mixtures through single-layer graphene oxide (GO) nanopores functionalized with COOH (carboxyl) and COO- (ionized carboxyl) groups. GO-COOH nanopore shows regular behavior with competitive permeation between the two species in the mixture. However, GO-COO- pore exhibits selective permeation of water, suggesting COO- functionalized GO sheets could provide the initial barrier to block ethanol permeation and enhance dehydration separation in GO-based membranes. Our simulation presents the underlying mechanism of the selective water transport is not determined by the pore-size sieving, but has been ascribed as the strong molecular affinity between water and GO-COO- surface. This interfacial interaction can induce the preferential interfacial adsorption and pore occupation for water, simultaneously impede the transport path of ethanol into the nanopore, and consequently give rise to the selective penetration of water in the mixture. The simulation results provide the direct theoretical evidence that ionization of carboxyl groups on GO sheets can be applied to improve the dehydration permeation of alcohol-water mixtures across GO-based separation membranes.