By the electrochemical lithiation of a Si(100) single-crystal substrate, regular quadrangular pyramidal shaped three-layered structures on Si(100) were observed in scanning electron microscopic images. Based on the results of soft X-ray emission spectroscopy and surface X-ray diffraction, it was concluded that these three layers consist of a single-crystalline Li15Si4 (sc-Li15Si4) alloy phase, an amorphous phase of Li15Si4 and/or Li13Si4 (a-Li15/13Si4) alloy, and a crystalline Si (c-Si) phase containing Li atoms formed on the Si(100) surface. When this was electrochemically delithiated completely, the first two layers, which appeared curled-up, changed to amorphous Si (a-Si) phase and the third layer to c-Si without Li atoms.