The geometric and electronic structures of several possible adsorption configurations of the pyrazine (C4H4N2) molecule covalently attached to Si(100) surface, which is of vital importance in fabricating functional nanodevices, have been investigated using X-ray spectroscopies. The Carbon K-shell (1s) X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of predicted adsorbed structures have been simulated by density functional theory (DFT) with cluster model calculations. Both XPS and NEXAFS spectra demonstrate the structural dependence on different adsorption configurations. In contrast to the XPS spectra, it is found that the NEXAFS spectra exhibiting conspicuous dependence on the structures of all the studied pyrazine/Si(100) systems can be well utilized for structural identification, which has been discussed in detail in this article. In addition, according to the classification of carbon atoms, the spectral components of carbon atoms in different chemical environments have been investigated in the NEXAFS spectra as well.