Ion transport is crucial for biological systems and membrane-based technology. Atomic-thick two-dimensional materials, especially graphene oxide (GO), have emerged as ideal building blocks for developing synthetic membranes for ion transport. However, the exclusion of small ions in a pressured filtration process remains a challenge for GO membranes. Here we report manipulation of membrane surface charge to control ion transport through GO membranes. The highly charged GO membrane surface repels high-valent co-ions owing to its high interaction energy barrier while concomitantly restraining permeation of electrostatically attracted low-valent counter-ions based on balancing overall solution charge. The deliberately regulated surface-charged GO membranes demonstrate remarkable enhancement of ion rejection with intrinsically high water permeance that exceeds the performance limits of state-of-the-art nanofiltration membranes. This facile and scalable surface charge control approach opens opportunities in selective ion transport for the fields of water transport, biomimetic ion channels and biosensors, ion batteries and energy conversions.