Molecular dynamics simulation is utilized in this project to numerically reproduce the filtration process of edge functionalized layer-by-layer graphene oxide membranes because they have a uniform structure to achieve superior separation performance. Water, NaCl, LiCl, and KCl solutions are separately filtrated. The edge functional groups, which include carboxyl, hydroxyl, and hydrogen are observed geometrically and interactionally affecting the membrane performance under the influence of membrane structures. Several mechanisms in which edge functionalized membrane could affect water transport and ion sieving performance are firstly uncovered. On those bases, strategies are proposed for better filtration performance in the future.