Electrocatalytic hydrodeoxygenation (EHDO) is a promising approach for upgrading biomass-derived bio-oils to sustainable fuels without the use of high-pressure hydrogen gas and elevated temperatures. However, direct EHDO for realistic hydrophobic lignin-based oil production remains challenging. Herein, we discuss the molecular dynamics that govern the EHDO of lignin bio-oil over Pt/C in an acidic electrolyte added with 2-propanol or a surfactant. Excellent conversion (98.1%) and a high yield (79.0%) of hydrogenated products, including 40.5% propyl-cyclohexane, are achieved under ambient temperature and pressure. Experimental results and various investigations on molecular dynamics suggest that EHDO occurs at the water-solvent-catalyst three-phase boundary. Proton transfer significantly influences the current density of EHDO. Factors such as cluster size and vector of lignin-based oil to electrode govern the selectivity and Faradaic efficiency of EHDO. This work advances the understanding of dynamics for EHDO and suggests governing factors to improve it.