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Metal-organic framework (MOF) nanoparticles are successfully confined in the hollow mesoporous carbon spheres (HMCSs) through space-confined synthesis methods. The prepared ZIF-67@HMCSs nanocomposites act as effective sacrificial templates, which can afford Co2+ sources. After a facile solvothermal reaction and sequential cation etching, yolk–shell-structured layered double hydroxide@HMCSs (LDH@HMCSs) have been synthesized. The LDH@HMCSs nanocomposite possesses a three-dimensional (3D) hollow nanocage superstructure that effectively blocks the self-stacking of LDH nanosheets and promotes ion transport. Compared to CoFe-LDH@HMCSs, and Co-LDH@HMCSs, CoNi-LDH@HMCSs exhibit superior electrochemical performance and desalination performance due to the remarkable synergistic effect between the CoNi-LDH nanosheets and mesoporous N-doped carbon shells. The resultant CoNi-LDH@HMCSs-0.4-based capacitive deionization (CDI) device exhibits excellent salt adsorption capacity (SAC, 36.41 mg·g–1) and good cycle stability. This work will confirm the significance of constructing superstructure and open new avenues for the practical application of CDI technology in water treatment.

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