Lithium-ion batteries are widely used to power portable electronics because of their high energy densities and have shown great promise in enabling the electrification of transport. However, the commercially used carbonate-based electrolytes are limited by a narrow operating temperature window and suffer against next generation lithium-ion battery chemistries such as silicon-containing anodes. The lack of non-carbonate electrolyte alternatives such as ether-based electrolytes is due to undesired solvent co-intercalation that occurs with graphitic anodes. Recently, fluorinated ether solvents have become promising electrolyte solvent candidates for lithium metal batteries but their applications in other battery chemistries have not been studied. In this work, we synthesize a group of novel fluorinated ether solvents and study them as electrolyte solvents for lithium-ion batteries. Using X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (ssNMR), we show that fluorinated ether electrolytes support reversible lithium-ion intercalation into graphite without solvent co-intercalation at conventional salt concentrations. To the best of our knowledge, they are the first class of ether solvents that intrinsically suppress solvent co-intercalation without the need for high or locally high salt concentration. In full cells using graphite anode, fluorinated ether electrolytes enable much higher energy densities compared to conventional glyme ethers, and better thermal stability over carbonate electrolytes (operation up to 60°C). As single-solvent-single-salt electrolytes, they remarkably outperform carbonate electrolytes with fluoroethylene carbonate (FEC) and vinylene carbonate (VC) additives when cycled with graphite-silicon composite anodes. Using X-ray photoelectron spectroscopy (XPS), NMR and density functional theory (DFT) calculations, we show that fluorinated ethers produce a solvent-derived solid electrolyte interphase, which is likely the key to suppressing solvent co-intercalation. Rational molecular design of fluorinated ether solvents will produce novel electrolytes that enable next generation lithium-ion batteries with higher energy density and wider working temperature window.