The desolvation of hydrated sodium ions (Na(H2O)x+) at the electrode/electrolyte interface is crucial for aqueous sodium-storage systems, but the rational regulation of desolvation process remains a significant challenge. Herein, a dual structural engineering strategies of electron configuration modulation and molecular intercalation for the regulation of desolvation kinetics between nitrogen-doped lamellar carbon-intercalated 1T-molybdenum disulfide (MoS2) superlattice nanoflower (1T-MoS2-NC) and Na(H2O)x+ is demonstrated. The synergy of cation-π interaction and adjustable interlayer structure induced by NC intercalation reduces the desolvation energy and promotes dehydration degree of Na(H2O)x+, thereby providing more interspace for Na+ accommodation. The abundant 1T metal phase accelerates the charge transfer while lowering the Na+ diffusion energy barrier. Benefitting from the advantages above, 1T-MoS2-NC exhibits superior capacitive deionization performance, including outstanding brackish water desalination capacity (80.9 mgNaCl g−1) and splendid long-term stability in a 1000 mg L−1 NaCl solution at a cell voltage of 1.4 V, which exceeds most of the state-of-the-art electrodes under similar experimental conditions. This finding reveals the facilitating effect of desolvation regulation on sodium-ion storage, paving the way for advanced electrochemical aqueous ion storage applications.