Residual Ca2+ decreases the efficiency and increases the power consumption of the chlor-alkali industry. However, Ca2+ and Na+ sieving is challenging due to the similar ionic radii of these cations. Inspired by the presence of carbonyl oxygens in key selective filters of biological Ca2+ and Na+ channels, we used molecular dynamics to investigate the effects of carbonyl oxygen atoms in modified graphene nanopores of various sizes (characteristic diameters: 0.57–1.50 nm) on Ca2+/Na+ sieving. The results demonstrated that selectivity is closely associated with the different roles of the carbonyl oxygen atoms. In small nanopores, Ca2+ sheds increased numbers of water molecules due to the predominant steric effect of carbonyl oxygen atoms. Thus, Ca2+ must overcome a higher energy barrier than Na+. This requirement prevents the passage of Ca2+. In large nanopores, carbonyl oxygen atoms do preferentially substitute water molecules outside the first hydration shell of Ca2+ compared with those outside the first hydration shell of Na+, thereby hindering Na+ departure from the nanopore. These findings provide useful guidance for the further development of Ca2+ separation materials as sensors and ion separators.