Molecular dynamics simulations were performed to obtain the two-dimensional pair correlation functions of Si(001) surface and deeper layers. The atoms interact via a potential developed by Stillinger and Weber, which includes both two-body and three-body contributions. The results show that the atoms in deeper layers still remain at their(001) atomic plane lattice sites, while the atoms in surface layer are rearranged, and a large part of them form bonding and the bond length is 0.2, 40nm. The relaxation problems have also been discussed.