Precise control of interlayer spacing and functionality is crucial in two-dimensional material based membrane separation technology. Here we show anion intercalation in protonated graphite phase carbon nitride (GCN) that tunes the interlayer spacing and functions of GCN-based membranes for selective permeation in aqueous/organic solutions. Sulfate anion intercalation leads to a crystalline and amphipathic membrane with an accessible interlayer spacing at ~10.8 Å, which allows high solvent permeability and sieves out the solutes with sizes larger than the spacing. We further extend the concept and illustrate the example of GCN-based chiral membrane via incorporating (1R)-(-)-10-camphorsulfonic anion into protonated GCN layers. The membrane exhibits a molecular weight cutoff around 150 among various enantiomers and highly enantioselective permeation towards limonene racemate with an enantiomeric excess value of 89%. This work paves a feasible way to achieve water purification and chiral separation technologies using decorated laminated membranes.