The separation of Co(II) and Ni(II) from leaching solution is gaining interest because Co(II) and Ni(II) are increasingly used in emerging strategic areas, such as power batteries. Herein, the surface of silica gel is functionalized with 1,2-ethylenediamine and used for the separation of Co(II) and Ni(II). The Co(II) removal efficiency of the modified silica is 80.2%, with a 4-fold improvement in the separation factor. The geometry, frequency, and electrostatic potential of the ethylenediamine modified silica gel (en/SG) are calculated. The corresponding properties of M2+(M-Co, Ni) adsorbed on en/SG in an aqueous solution are simulated and analyzed. The results show that ethylenediamine tends to form [Men(H2O)4]2+after binding to M2+, and the binding ability of Co(II) to ethylenediamine is stronger. Besides, the thermodynamic calculations show that en/SG has a more negative Gibbs free energy when absorbing Co(II) in aqueous solution, so en/SG is more inclined to bind with Co(II) preferentially. It is the difference in complexation ability between Ni, Co, and ethylenediamine that enlarges the difference in the original physical adsorption, thus strengthening the separation performance. This work will provide guidance for a rational design of high-performance nickel-cobalt adsorption materials.