The two-dimensional conjugated organic small-molecule triquinoxalinylene derivative tribenzoquinoxaline-5,10-dione (3BQ) has demonstrated significant potential for cathodes in secondary batteries. However, the exploration depth regarding the disparity in initial capacity between its cathodes for Na-ion batteries (NIBs) and Li-ion batteries (LIBs) remains limited. Herein, the adsorption processes of Na⁺ and Li⁺ within the confined redox-active sites of 3BQ were simulated through first-principles calculations. The findings reveal that the arrangement of ions with diverse radii is regulated by the inflexible structure of 3BQ molecules, resulting in distinct variations in their respective adsorption processes. Furthermore, cyclic voltammetry tests were performed to verify the predicted platform potentials and discharge capacities of the three stages. This study aims to gain a better understanding of how organic molecules with multiple active sites regulate ions with different radii. By investigating the selectivity of organic molecules towards ions, we hope to provide insights for designing organic molecules with multiple redox-active sites.