The chemisorption and decomposition of thiophene (C4H4S) and furan (C4H4O) on the reconstructed Si(100)-2 × 1 surface has been investigated by means of the hybrid density functional (B3LYP) method in combination with a cluster model approach. Two chemisorption mechanisms, i,e., [4 + 2] and [2 + 2] cycloadditions of C4H4X (X = S,O) onto a surface dimer site, have been considered comparatively. The calculations revealed that the former process is barrierless and favorable over the latter, which requires a small activation energy (2.6 kcal/mol for thiophene and 1.2 kcal/mol for furan). The di-σ bonded surface species formed by [4 + 2] cycloaddition-type chemisorption can either undergo further [2 + 2] cycloaddition with a neighboring Si=Si dimer site, giving rise to a tetra-σ bonded surface species, or undergo deoxygenation (desulfurization) by transferring the heteroatom to a neighboring Si=Si dimer site, leading to a six-member ring metallocyclic C4H4Si2 surface species. The latter process was found to be slightly more favorable than the former, especially in the case of thiophene.