Fluoroethylene carbonate (FEC)-based electrolytes using FEC as the co-solvent (50 wt%) are investigated and compared with the electrolyte using FEC as the additive (10 wt%) for freestanding Si-carbon nanotubes (CNTs) composite paper anodes for Li-ion batteries. The ethylene carbonate (EC)-free FEC-based electrolyte is found to achieve higher specific capacity and better capacity retention in terms of long-term cycling. After 500 cycles, the capacity retention of the cell using diethyl carbonate (DEC)-FEC (1:1 w/w) is increased by 88% and 60% compared to the cells using EC-DEC-FEC (45:45:10 w/w/w) and EC-FEC (1:1 w/w), respectively. Through SEM-EDX and XPS analyses, a possible reaction route of formation of fluorinated semicarbonates and polyolefins from FEC is proposed. The inferior cell performance related to the EC-containing electrolytes is likely due to the formation of more polyolefins, which do not favor Li ion migration.