Octahedral molecular sieves (OMSs) based on MnO2 have been widely studied in the fields of deionization, geochemistry, and energy storage due to their microporous tunnel framework capable of adsorbing and exchanging various ions, particularly cations. The understanding of cation adsorption/exchange within OMS tunnels demands atomic-scale exploration, which has been scarcely reported. Here, we disclose how various cations (K+/Ag+/Na+) interplay within the OMS tunnel space on an atomic scale. Not only are the lattice sites for each adsorbed cation species pinpointed but the scenario of dual-cation adsorption within single tunnels is also demonstrated, together with the discovery of characteristic concentration-dependent cation ordering. Moreover, compared with the theoretical parent tunnel phase, the heterogeneous tunnels, though sparsely distributed, exhibit a distinct yet orderly cationic accommodation, highlighting the non-negligible role of tunnel heterogeneity in regulating OMS physiochemistry. Our findings clarify the long-existing ambiguities in nano- and atomic-scale science of the ion adsorption process in OMS materials and are expected to inspire their structural/compositional engineering toward functionality enhancement in various fields.