Layered manganese dioxide (δ-MnO₂) is considered a promising ammonium ion capture electrode material for capacitive deionization (CDI) attributed to its high theoretical capacity and cost-effectiveness. Nevertheless, it continues to encounter challenges including rapid capacity degradation, structural instability, and Jahn–Teller effect. Herein, a crystal and electron synergistically regulation engineering strategy is proposed for the suppression of the Jahn–Teller effect and the improvement of ammonium ion storage dynamics in F doped MnO₂ (MnOF). The induced action of F ions transforms the MnO₂ structure from the original cubic [MnO₆] octahedron into an asymmetric [Mn(OF)₆] octahedron with electron redistribution, and generates a localized charge imbalance along the O–Mn–F pathway, which promotes electron transfer from Mn to F direction, accelerates electron transfer, and reduces the energy barrier of ammonium ion diffusion. As a result, the prepared MnOF exhibited a maximum salt adsorption capacity of 144.3 mg g⁻¹ and an exceptionally high salt adsorption rate of 18.25 mg g⁻¹ min⁻¹, along with outstanding cycling stability. Besides, ex/in situ characterizations reveal that in MnOF, the formation/breaking of hydrogen bond is accompanied by the insertion/deinsertion of NH₄⁺. Therefore, the rational introduction of highly electronegative anions provides a new direction for the development of advanced CDI electrode materials.