The separation behaviors of Mg2+ and Li+ were investigated using molecular dynamics. Two functionalized graphene nanopore models (i.e., co_5 and coo_5) inspired by the characteristic structural features of Mg2+ channels were used. Both nanopores exhibited a higher preference to Mg2+ than to Li-+,Li- and the selectivity ratios were higher for coo_5 than for co_5 under all the studied transmembrane voltages. An evaluation of the effect of coordination on the ionic hydration microstructures for both nanopores showed that the positioning of the modified groups could better fit a hydrated Mg2+ than a hydrated Li+, as if Mg2+ was not dehydrated according to hydrogen bond analysis of the ionic hydration shells. This condition led to a lower resistance for Mg2+ than for Li+ when traveling through the nanopores. Moreover, a distinct increase in hydrogen bonds occurred with coo_5 compared with co_5 for hydrated Li+, which made it more difficult for Li+ to pass through coo_5. Thus, a higher Mg-2/Li+ selectivity was found in for coo_5 than for co_5. These findings provide some design principles for developing artificial Mg2+ channels, which have potential applications as Mg2+ sensors and novel devices for Mg2+/Li+ separation.