<p>Atomically thin graphene membranes with sub-1-nm pores show promise for ion/molecular separation, osmotic energy generation, and energy storage. Narrowing the pore size distribution and controlling the surface charge are essential to achieve these applications. However, nanoporous graphene membranes fabricated via conventional methods possess a broad pore size distribution and inadequately regulated surface charge, limiting their applications. Herein, we present a molecular anchoring approach for scalable synthesis of nanoporous graphene membranes via a bottom-up technique, aiming to narrow the pore size distribution without reducing the pore density while simultaneously adjusting the charge properties of nanopores. By selecting suitable anchoring molecules, the custom-tailored pore size distribution and chemical functionality of nanoporous graphene membranes can be achieved. Leveraging the steric restriction effect, anchoring monomers selectively traverse larger nanopores to form ion-selective plugs, effectively repairing these nanopores. The centimeter-scale nanoporous graphene membrane with an ion-selective plug achieves high separation selectivity (K⁺/Na⁺=20, K⁺/Mg²⁺=330). Theoretical simulations indicate that a smaller pore size, narrow pore size distribution, and positive charge result in a larger energy barrier difference, leading to ultrahigh metal ion selectivity. Furthermore, in treating lithium battery leaching solutions, Li⁺/divalent ions selectivity exceeds 900. These findings provide a way for designing graphene-based membranes.</p>