Microstructural characteristics of passive films on highly oriented pyrolytic graphite (HOPG) lithiated in siloxane-based electrolytes dissolving lithium bis(oxalato) borate (LiBOB) were analyzed. Scanning electron microscopy (SEM) images of the lithiated HOPG showed island-like deposition on the basal planes and film-like deposition on edge planes. X-ray spectroscopy revealed that the film-like deposition exhibited higher concentrations of Si and O than the island-like deposition. Fourier transformation infrared (FT-IR) spectroscopy of the siloxane-based electrolyte and the HOPG surface indicated consumption (decomposition) of LiBOB salt and bond breakage between the siloxane backbone and ethylene oxide side chain function groups. Based on FT-IR spectra from the lithiated graphite surface, the assigned function groups in the products included the flexible groups –Si–O– and –C–O–. These flexible function groups are expected to absorb the volumetric changes in graphite particles during lithiating and delithiating in an electrochemical cell, which will prevent continuous decomposition of siloxane electrolyte on the graphite surface.