We investigated the influence of the anions in ionic liquid electrolytes on the electrochemical performance of a silicon (Si) negative electrode for a lithium-ion battery. While the electrode exhibited poor cycle stability in tetrafluoroborate-based and propylene carbonate-based electrolytes, better cycle performance was achieved in bis(fluorosulfonyl)amide (FSA–)- and bis(trifluoromethanesulfonyl)amide (TFSA–)-based electrolytes, in which the discharge capacity of a Si electrode was more than 1000 mA h g−1 at the 100th cycle. It is considered that a surface film derived from FSA–- and TFSA–-based electrolytes effectively suppressed continuous decomposition of the electrolyte. In a capacity limitation test, a discharge capacity of 1000 mA h g−1 was maintained even after about the 1600th cycle in the FSA–-based electrolyte, which corresponds to a cycle life almost twice as long as that in TFSA–-based electrolyte. This result should be explained by the high structural stability of FSA–-derived surface film. In addition, better rate capability with a discharge capacity of 700 mA h g−1 was obtained at a high current rate of 6 C (21 A g−1) in FSA–-based electrolyte, which was 7-fold higher than that in TFSA–-based electrolyte. These results clarified that FSA–-based ionic liquid electrolyte is the most promising candidate for Si-based negative electrodes.