Monofluoroethyl methyl carbonate (F1EMC) is demonstrated as an effective fluorinated co-solvent for high-voltage sodium-ion batteries. Molecular dynamics (MD) simulations coupled with Fourier-transform infrared spectroscopy (FTIR) reveal that F1EMC promotes preferential PF6− anion aggregation relative to conventional ethyl methyl carbonate (EMC), shifting the solvation shell toward anion-dominated coordination. With 2% fluoroethylene carbonate (FEC) additive, ∼200 mAh Na0.97Ca0.03[Mn0.39Fe0.31Ni0.22Zn0.08]O2 (NCMFNZO)/hard carbon (HC) pouch cells retain over 80% capacity after 300 cycles at 40 °C and 4.0 V. Electrochemical impedance spectroscopy, X-ray photoelectron spectroscopy, soft X-ray absorption spectroscopy, and electron microscopy collectively identify a NaF-rich, chemically protective cathode–electrolyte interphase (CEI) as the origin of improved performance. MD and density functional theory (DFT) calculations confirm that enhanced PF6− aggregation drives preferential anion decomposition at the cathode surface, mechanistically accounting for NaF enrichment. This work establishes partial co-solvent fluorination as a rational electrolyte design strategy for high-voltage sodium-ion batteries.