A comprehensive understanding of the charge/discharge behaviour of high-capacity anode active materials, e.g., Si and Li, is essential for the design and development of next-generation high-performance Li-based batteries. Here, we demonstrate the in situ scanning electron microscopy (in situ SEM) of Si anodes in a configuration analogous to actual lithium-ion batteries (LIBs) with an ionic liquid (IL) that is expected to be a functional LIB electrolyte in the future. We discovered that variations in the morphology of Si active materials during charge/discharge processes is strongly dependent on their size and shape. Even the diffusion of atomic Li into Si materials can be visualized using a back-scattering electron imaging technique. The electrode reactions were successfully recorded as video clips. This in situ SEM technique can simultaneously provide useful data on, for example, morphological variations and elemental distributions, as well as electrochemical data.