Glass ceramics containing Na super-ionic conductor (NASICON) crystals are promising candidates for solid-state electrolyte separators in aqueous sodium ion batteries due to their high ion conductivity, water stability, and productivity. Our objective was to fabricate a glass-ceramic separator by crystallizing a NASICON phase within the glass via heat-treatment. We conducted a detailed investigation into the structural evolution of the glass and the crystallization morphology. Upon heat-treatment, Si units polymerized to form an island-like phase, while P contributed to increasing non-bridging O to form a sea-like phase during droplet phase separation; subsequently, the Na2Zr2SiP2O12 crystalline phase formed. The remaining glass comprised Q4 units of Si in the island-like phase, and Q1 and Q2 units of P in the sea-like phase. The ionic conductivity of the sample increased by crystallization up to 5.4 × 10–5 S⋅cm –1 at 300 K. Furthermore, the water leakage tests showed that both the glass and glass-ceramics exhibited low leakages.