The “battery type” inorganic electrode has been demonstrated the highly efficient sodium ion intercalation capacity for capacitive deionization. In this work, the CoMn2O4 (CMO) microspheres with porous core‐shell structure are prepared via co‐precipitation and followed by annealing. The effects of annealing temperatures on the morphology, pore structure, valence state, and electrochemical behavior of CMO are explored. As electrode for capacitive deionization, the salt removal capacity and current efficiency of optimized AC || CMO device reaches up to 60.7 mg g−1 and 97.6%, respectively, and the capacity retention rate is 74.1% after 50 cycles. Remarkably, both the in‐situ X‐ray diffraction and ex‐situ X‐ray diffraction analysis features that the intercalation/de‐intercalation of sodium ions are governed by (103) and (221) crystal planes of CMO. Accordingly, the density functional theory calculations realize that the adsorption energies of Na+ onto (103) and (221) crystal planes are higher than that of any other crystal planes, manifesting the priorities in adsorption of sodium atoms. Furthermore, the X‐ray photoelectron spectra of pristine and post‐CMO electrode highlights that the reversible conversion of Mn3+/Mn4+ couple is resulted from the intercalation/de‐intercalation of Na+, while this is irreversible for Co3+/Co2+ couple. Beyond that, the CMO electrode has been proven the selectivity removal of Na+ over K+ and Mg2+ in a multi‐cation stream.