Abstract: Electrochemical reduction technology offers mild reaction conditions and easy modular integration, showing great application potential for mercury resource recovery. However, traditional two-electrode systems often suffer from hydrogen evolution caused by cathode potential drift, as well as re-oxidation of mercury due to the migration of anodic oxidizing species in a single-chamber solution. To address these issues, this study innovatively constructed a three-electrode dual-solution system employing hydrophobic carbon paper as the cathode, a nickel sheet as the anode, and Hg/Hg2SO4 reference electrode. A bipolar membrane was introduced to separate the anodic and cathodic chambers, enabling precise control of the cathodic potential and physical isolation of the redox environments. COMSOL-based multiphysics simulations were further conducted to analyze the coupled transport and electrochemical processes. The results revealed that the system achieved a mercury recovery of 75.45% and a Faradaic efficiency of 80.23% under the conditions of a deposition potential of –0.42 V, reaction time of 1.5 h, stirring rate of 300–400 r/min, temperature of 30 °C, and initial Hg2+ concentration of 300–400 mg/L. Meanwhile, the simulation further revealed that the flow rate increasement could significantly alleviate concentration polarization and enhanced mass transfer, whereas a more negative cathode potential preferentially triggered the hydrogen evolution reaction at the electrode edge region due to a sharp increase in local current density, leading to uneven deposition.