During fast-charging, uneven lithium plating on the surface of commercial graphite anode impedes the electrochemical performance of lithium-ion batteries, causing a safety issue. The formation of a passivation layer, the solid-electrolyte interphase (SEI), due to side reactions with the organic electrolyte, correlates with long-term cycling performance under fast-charging conditions, necessitating comprehensive analysis. Herein, it is demonstrated that a molybdenum disulfide (MoS<sub>2</sub>) coating on natural graphite (NG) modulates the properties of the SEI layer, enabling reduction of the charging time and the enhancement of long-term cycling performance. MoS<sub>2</sub> spontaneously transforms into Li<sub>2</sub>S and Mo nanoclusters through intercalation and conversion with Li<sup>+</sup>, altering the chemical composition and stability of the SEI layer on the NG, promoting faster Li<sup>+</sup> transport, and reducing interfacial resistance. The MoS<sub>2</sub>-NG anode shows improved fast-charging capability and cycling performance under 3.0 C-charging and 1.0 C-discharging over 300 cycles without compromising energy density. In the full-cell configuration, a charging time of 14.7 min at 80% state of charge is achieved, making it suitable for electric vehicle applications.