Laminated graphene oxide (GO) membrane has great attention for ultrafast flux membrane with well-defined pore structure. However, laminated structure is sensitive to various factors such as functionalization, fabrication method and especially support morphology due to ultrathin thickness. Herein, we investigated surface roughness effect by controlling systematically wrinkled structure of support with ion beam treatment. Wrinkled surface of support generates free volume at interface, facilitating fast water transport, which confirmed 6.4 times enhancement on permeation of water while maintaining high rejection of all dye molecules. The tunability of nanostructure through support control can provide development for ultrathin GO membrane in water purification.