Urchin-like MnO₂ polymorphs (α-, β-, and γ-) were successfully synthesized via a hydrothermal method with precise parameter optimization using a factorial design. This study provides the first comprehensive exploration of how tunnel-phase structures influence desalination performance in hybrid capacitive deionization. Among these polymorphs, α-MnO₂ exhibited the most uniform urchin-like morphology with larger [2 × 2] tunnel structures, facilitating optimal ion transport and enhanced electrochemical properties. Electrochemical evaluations revealed that α-MnO₂ achieved the highest specific capacitance of 148 F/g at 5 mV/s, significantly outperforming β-MnO₂ and γ-MnO₂. For desalination applications, α-MnO₂ demonstrated a record-high NaCl adsorption capacity of 24.4 mg/g at 1.4 V, surpassing the performance of γ-MnO₂ (14.5 mg/g) and β- MnO₂ (5.5 mg/g). These findings underscore the transformative potential of α-MnO₂, showcasing its scalability and applicability for next-generation water treatment and energy storage systems.