Based on electron microscope techniques developed for ionic liquids (ILs), which have both high stability under vacuum and an antistatic nature, specially-designed Li battery cells with all components contained in actual Li batteries were fabricated for in situ electron microscope observation. Various interesting anode behaviors in the Li battery were observed. For example, Si thin flake active material can store Li(I) electrochemically, causing the morphology to change into a ribbon-like or isotropic expanded structure. Surprisingly any damage to the Si material was not recognized by nanoscale imaging because of the thin layer structure that can release internal stress spontaneously during lithiation. In addition, the Li metal deposition process was directly observed and a similar approach can be applied to in situ X-ray photoelectron spectroscopic analysis.