The effect of fluoroethylene carbonate (FEC) as a co-solvent on electrochemical battery performance and surface chemistry was investigated at nano-sized amorphous molybdenum dioxide (a-MoO2) lithium-ion secondary battery negative electrodes. The capacity retention was enhanced as a function of the FEC concentration up to approximately 7% after 50 cycles. The surface characterization conducted by EIS, FE-SEM, FT-IR, and XPS revealed that the improved battery performance of the a-MoO2 was attributed to the modification of the surface chemistry depending on the FEC content. An ion conductive, mechanically and electrochemically stable, and thin solid electrolyte interphase (SEI) was developed as a result of successive reductive decomposition of FEC at the a-MoO2 surface. The superior film properties originated from the FEC-reduced products that were rich in polycarbonates and LiF. Based on the findings, SEI formation mechanisms for ethylene carbonate (EC)-derived, FEC-derived, and EC-/FEC-co-derived SEI were also developed. Identification of the mechanisms proposed herein could provide a good understanding of the FEC effect in modifying the surface reaction of typical lithium-ion secondary battery negative electrodes.