Reverse osmosis (RO) membranes are widely used as energy-saving and environmentally friendly materials for water purification. This Focus Review reports on the nanoscale structure and permeation mechanism of crosslinked fully aromatic polyamide RO membranes. First, the research on the morphology of protuberance structures of the polyamide separation functional layer is described. Next, hydrated structure of the functional layer is focused, which was analyzed using neutron scattering and molecular dynamics simulations. Innovative RO membranes are being developed that can obtain higher quality water with less energy by precisely controlling nanostructures.