Herein, a functionalized nanoporous graphene (FNG) membrane was developed to mitigate the contemporary issues affecting graphene oxide (GO) membranes, such as the low flux induced by its long tortuosity and poor membrane stability in aqueous solvents. GO was thermally activated at 650 °C to prepare a nanoporous carbon sheet with a turbostratic structure (pore size < 4 nm). Thereafter, the nanoporous graphene (NG) was consecutively functionalized with oxygen-containing groups by KMnO4 treatment and re-dispersed in water to deposit an FNG layer on a porous polymeric support. The FNG membrane exhibited ultrafast water permeance (586 Lm-2h-1bar-1) and precise molecular separation (molecular weight cut off: 269 Da). The membrane performance surpasses the upper bound of previously reported polymers and two dimensional-material-based nanofiltration membranes by the synergistic effect of nanopores and oxygen-containing groups. Furthermore, the practical operation of the FNG membrane is feasible under cross-flow, and water-flux decline by filtered molecules is highly suppressed by the presence of abundant nanopores as compared to conventional GO membranes.