We investigate the initial stage of the C incorporation into Si(001) using thermal dissociation of C2H2. The scanning tunneling microscopy shows that C-induced dimer vacancies (DVs) with depressed adjacent dimers are generated on the surface and aligned in the dimer direction, forming the 2xn structure. The ab initio pseudopotential calculations reveal that, with the presence of a DV in the surface, the alpha site in the fourth subsurface layer directly below the DV is the most favorable for the incorporated C atoms. The embedded C atoms align one dimensionally due to the interaction which is attractive in neighboring dimer rows but repulsive in the same dimer row.