High-purity rare earth elements (REEs) are critical for many modern technologies. However, the current industrial solvent extraction process is energy-intensive and environmentally unfriendly due to inadequate selectivity and the toxicity of ligands. Methods combining both size effects and binding affinity can promote separation among lanthanides, but the effect of long-range confinement is largely unexplored. Here we proposed and designed a new platform to achieve separation among lanthanides directly in aqueous systems without any ligands using extremely confined manganese oxide (MnO₂) solid ionic channels. We have successfully achieved separation using both ion exchange and electrochemical intercalation methods. No one has ever used electrochemical intercalation for the separation of REEs and this will impact REE’s supply security by enabling efficient separation of REEs without the use of harsh chemicals which only requires the input of electricity. Based on our understanding of (de)hydration, we are able to change the confinement level to further boost the selectivity. The molecular design principles for optimizing ion coordination in a confined solid matrix can be translated to other material systems and to the separation of actinides and other multivalent metals valuable for energy technologies.