We evaluated the charge–discharge behavior of four types of graphite electrode, including raw synthetic graphite (SG), shaped natural graphite (NG), soft carbon-coated natural graphite (SCNG), and hard carbon-coated natural graphite (HCNG), in a 1-ethyl-3-methylimidazolium bis(fluorosulfonyl)imide (EMImFSI) ionic liquid. Based on the charge–discharge curves for the first cycle in LiTFSI/EMImFSI, capacity loss arising from an irreversible reaction on the graphite anodes was clearly observed for the cells consisting of SG and SCNG, whereas the capacity loss for the cells containing NG and HCNG was relatively low. The coulombic efficiency during cell cycling also confirmed that the charge–discharge behavior of graphite in LiTFSI/EMImFSI is strongly affected by the surface structure of the graphite and that basal-plane-oriented graphite, such as NG and HCNG, can reduce the primary charge capacity loss. The advantages of the stable charge–discharge behavior provided by FSI-based ionic liquids for lithium ion batteries are also discussed based on the application of voltammetric and electrochemical impedance techniques to model carbon electrodes in ionic liquids. Based on these analyses, a mechanism involving a double-layer-based interface (not a solid electrolyte interface (SEI)) is proposed to stabilize the surface of graphite negative electrodes.