Due to its exceptional lithium storage capacity silicon is considered as a promising candidate for anode material in lithium-ion batteries (LIBs). In the present work we demonstrate that methods of the soft X-ray emission spectroscopy (SXES) can be used as a powerful tool for the comprehensive analysis of the electronic and structural properties of lithium silicides Li$_{x}$Si forming in LIBs anode upon Si lithiation. On the basis of density functional theory (DFT) and molecular dynamics (MD) simulations it is shown that coordination of Si atoms in Li$_{x}$Si decreases with increase in Li concentration both for the crystalline and amorphous phases. In amorphous a-Li$_{x}$Si alloys Si tends to cluster forming Si-Si covalent bonds even at the high lithium concentration. It is demonstrated that the Si-L$_{2,3}$ emission bands of the crystalline and amorphous Li$_{x}$Si alloys show different spectral dependencies reflecting the process of disintegration of Si-Si network into Si clusters and chains of the different sizes upon Si lithiation. The Si-L$_{2,3}$ emission band of Li$_{x}$Si alloys become narrower and shifts towards higher energies with an increase in Li concentration. The shape of the emission band depends on the relative contribution of the X-ray radiation from the Si atoms having different coordination. This feature of the Si-L$_{2,3}$ spectra of Li$_{x}$Si alloys can be used for the detailed analysis of the Si lithiation process and LIBs anode structure identification.