The reaction dynamics of ethylene adsorption onto the Si(001) surface have been studied by combining density functional theory-based molecular dynamics simulations with molecular adsorption sampling scheme for investigating all kinds of reaction pathways and corresponding populations. Based on the calculated results, three possible reaction pathways—the indirect adsorption, the direct adsorption, and the repelling reaction—have been found. First, the indirect adsorption, in which the ethylene (C2H4(ads)) forms the π-bonded C2H4(ads) with the buckled-down Si atom to adsorb on the Si(001) surface and then turns into the di-σ-bonded C2H4(ads), is the major reaction pathway. The short-time Fourier transform analysis of structural coordinate autocorrelation function is performed to further investigate the evolution of different vibrational modes along this indirect reaction pathway. This analysis illustrates that the Infrared (IR) inactive peak of the CC stretching mode of the π-bonded C2H4(ads) shifts to the IR inactive peak of the CC stretching mode of di-σ-bonded C2H4(ads), which is in a good agreement with the IR inactive peak of the CC stretching mode vanished in the vibrational spectrum at 150 K (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Second, the direct adsorption, in which the di-σ-bonded C2H4(ads) is formed directly with the Si intradimer or the Si interdimer on the Si(001) surface, is the less significant reaction pathway. This reaction pathway leads to the CC stretching mode and the CH stretching mode of the di-σ-bonded C2H4(ads) appeared in the vibrational spectra at 48 and 150 K, respectively (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Finally, the repelling reaction, in which the C2H4(g) first interacts with the Si dimer and then is repelled by Si atoms, is the least important reaction pathway. Consequently, neither the π-bonded C2H4(ads) nor the di-σ-bonded C2H4(ads) is formed on the Si(001) surface. © 2013 Wiley Periodicals, Inc.