The periodic density functional theory (periodic DFT) method was employed for the interpretation of infrared radiation spectra (IR spectra) measured for the hydrogen-covered H/Si(100) surface after the standard step of native oxide removal by brief etching in 40% NH4F. The IR employed the attenuated total reflectance (ATR) method. The periodic DFT calculations of IR spectra focused on reconstructions of H/Si(100) that involved combinations of surface-terminating Si–H groups including the double-occupied dimer (DOD), dihydride (DH), and trihydride (TH). The IR spectra calculated with periodic DFT for H/Si(100) surfaces were compared with the IR spectra calculated by means of DFT in Si–H clusters. The periodic DFT provided considerably better and more reliable theoretical description of the IR spectra by keeping the periodicity of the silicon material that guaranteed proper spatial distribution of the Si–H species within H/Si(100). The calculated IR spectrum for H/Si(100) that involved a combination of two DOD and three DH groups (7 × 1 reconstruction) was in good agreement with the measured IR spectrum. Moreover, a combination of the calculated IR spectra for DH in 1 × 1 reconstruction and the spectra for adjacent DH and DOD in 3 × 1 reconstruction (no long-range ordering) also agreed with the experiment. The periodic DFT further indicated that the IR peaks measured above 2120 cm–1 can originate in mutual steric interactions of adjacent DH species within H/Si(100). Accordingly, we hypothesize that the H/Si(100) surface prepared by the standard treatment likely involves combinations of DOD and DH but not TH.