The CASTEP ab initio calculation was coupled with TEM-EELS analysis to elucidate the nanostructural change of Si during Li+ insertion. Even if the previous research alleged that Si should change into amorphous lithium silicide in the initial stage of Li+ insertion, our observation let us know that during the electrochemical Li+ insertion, Si transforms into LiSi with medium-range ordering, and finally into a well-known crystalline phase, Li15Si4. Because some macroscopic observation (such as the volume expansion and charge-discharge behaviors) is almost in accordance with the microstructural analysis for this clarified phase transition, we can say that the correlation between experimental edge spectra and theoretical calculation based on density functional theory is very meaningful way to clarify the phase transition of materials.