3D covalent−organic framework (3D COF) membranes have unique features such as smaller pore sizes and more interconnected networks compared with 2D COF counterparts. However, the complicated and unmanageable fabrication hinders their rapid development. Molecular simulation, which can efficiently explore the structure-performance relationship of membranes, holds great promise in accelerating the development of 3D COF membranes. In this study, a series of 3D-COF membranes (TFPM-Pa-X) is designed with different charge densities (fully charged, partially charged, and neutral) and interpenetration numbers (2-, 3-, 4-, and 5-fold), subsequently investigate their contributions to Li⁺/Mg²⁺ separation through molecular simulation. Membrane morphology and pore size are found to strongly depend on the charged density and interpenetration number. The pore size and Cl⁻ ion density play a crucial role in governing membrane separation performance. TFPM-Pa-X membrane with a smaller interpenetration number and a higher charge density promotes Li⁺/Mg²⁺ separation. The fully charged 2-fold interpenetrated membrane has superior performance in breaking the trade-off between the flux of Li⁺ (J_Li⁺) and the selectivity of Li⁺ over Mg²⁺ (S_Li⁺_/Mg²⁺). This study may facilitate the rational design of new 3D COF membranes for high-performance ion separation.