Rechargeable magnesium batteries are regarded as a promising multi‐valent battery system for low‐cost and sustainable energy storage applications. Boron‐based magnesium salts with terminal substituent fluorinated anions (Mg[B(ORF)4]2, RF = fluorinated alkyl) have exhibited impressive electrochemical stability. Nevertheless, their deployment is hindered by the complicated synthesis routes and the surface passivation of Mg anode. Herein, we report the design of an advanced electrolyte formulation comprised of B(HFIP)3 and I2 in 1,2‐dimethoxyethane (DME), which eventually convert into a Mg[B(HFIP)4]2/DME‐MgI2 electrolyte system upon interacting with Mg anode. The Mg anode reacts with I2 and the electron‐accepting B(HFIP)3, leading to the in‐situ formation of a solid‐electrolyte interphase layer composed of MgF2 and MgI2 species that can facilitate fast and stable Mg plating/stripping. Compared with the pristine Mg[B(HFIP)4]2/DME electrolyte, the Mg[B(HFIP)4]2/DME‐MgI2 electrolyte exhibited superior electrochemical performance including an ultra‐low overpotential (~80 mV), high Coulombic efficiency and a long‐cycling period over 1500 h. In result, the rechargeable magnesium batteries with Mg[B(HFIP)4]2/DME‐MgI2 electrolyte and Mo6S8 cathode show outstanding compatibility, rapid kinetics, and stable cyclability for over 1200 cycles, surpassing all previously reported boron‐based electrolytes. This work introduces a promising halogen‐enhancement strategy for boron‐based Mg‐ion electrolytes and is pivotal for the advancement and optimization of multi‐valent secondary batteries.