We discuss here carboxylate graphene nanopore adsorbed with bivalent cations for Mg²⁺/Li⁺ separation based on molecular dynamic simulations. The results show that these graphene nanopores exhibit higher permeating preference to Li⁺ than to Mg²⁺, with the Mg²⁺/Li⁺ ratio down to 0.2–0.5, even when the pristine hole diameter is larger than 2 nm. The Li⁺ selectivity can be attributed to the block of ion hydration layers and ion association. The distribution analyses of ion in the nanopore indicate that Li⁺ can be closer to Ca²⁺ of nanopores, and the looser hydration layers of Li⁺ make it be less blocked by the hydration layers of Ca²⁺, resulting in the larger available area in the nanopore for Li⁺ to transport. The ion association of Mg²⁺ or Li⁺ with Cl⁻ can be enhanced near nanopores, the stronger ion association of Mg²⁺ with Cl⁻ leads to a stronger permeating resistance for Mg²⁺. This work displays the possibility of high lithium ion selectivity in large graphene nanopores, which can lower the cost of graphene perforation, and may provide inspiration for further efficient extraction of Li⁺ from salt-lake brines.