Lithium metal batteries (LMBs) hold great promise in facilitating high-energy batteries due to their merits such as high specific capacity, low reduction potential, and so forth. However, the realizations of practical LMBs are hindered by severe problems such as undesirable dendrite growth, poor Coulombic efficiency, and so forth. A recently proposed fluorinated electrolyte based on 1 M lithium bis(fluorosulfonyl)imide (LiFSI) dissolved in designed fluorinated 1,4-dimethoxybutane (FDMB) solvent has attracted significant attention because of its excellent electrochemical performance that origins from its superior physical and chemical properties, especially its unique ability in forming a robust, stable solid electrolyte interphase (SEI). However, the detailed structure and reaction mechanism of the SEI formation in such a novel electrolyte remains unclear. In this work, we carry out a hybrid ab initio and reactive molecular dynamics (HAIR) simulation to investigate the elementary reactions that regulate the formation of the primitive SEI, paying special attention to the process that involves FDMB, the fluorinated solvent. HAIR simulation reveals that both FSI − anion and FDMB provide F that is adequate to form a uniformed LiF layer that resembles the inorganic inner layer (IIL) of the SEI. N and S radicals from the FSI − anion, which do not deposit on the electrode interface to form lithium-containing inorganic substances, promote the polymerization reaction of unsaturated carbon chains produced by FDMB defluorination, forming the organic outer layer (OOL) of the SEI. The combination of the LiF-rich IIL and polymer-rich organic OOL explains the superior performance of the FDMB-based electrolyte in the device. The detailed reaction mechanism and SEI observed in this work provide insights into the atomic scale for the rational design of F-rich electrolytes in the near future.