Hybrid ion conductors that transport multiple ionic conductive species provide a useful platform for understanding how mixed-ion transport governs ionic conductivity within a single phase. However, the controlled introduction of multiple mobile ions into solid-state electrolytes and a mechanistic understanding of their migration within the framework remain challenging. Herein, a skeleton-retained Li⁺↔Na⁺ cationic exchange was used to simultaneously induce Li⁺ and Na⁺ cations into the NASICON-type framework of Li_3–xNa_xZr₂Si₂PO₁₂ (0 < x < 3). We show that the interpenetration of NaO₆ and NaO₈ coordination polyhedra significantly influences the ionic conductivity of hybrid ion conductors. Computational analysis indicates that Na⁺ transfer from octahedral NaO₆ sites to octa-coordinated NaO₈ sites is thermodynamically favorable, accompanied by Li⁺ relocation from NaO₈ to tetrahedral LiO₄ environments at former NaO₆ sites, thereby promoting Li⁺/Na⁺ site segregation. The increased occupation of Na⁺ at NaO₈ sites not only suppresses Na⁺ mobility due to bottleneck limitations but also hinders the formation of a continuous Li⁺ migration network, thereby reducing the room-temperature ionic conductivity from 1.78 to 0.50 mS·cm^–1. Upon re-exchange, Na⁺ in the NaO₈ sites is replaced by Li⁺ in penta-coordinated LiO₅, which re-establish percolating ion-transport pathways for Li⁺ and enable reversible recovery of the overall conductivity. These results reveal a fast dual-ion conduction mechanism enabled by the interpenetrating occupation of Li⁺ and Na⁺ across the available sites. This work opens a new avenue for the development of hybrid ion conductors.