Density functional theory was used to investigate the adsorption and reaction of HfCl4 with two hydroxyls on Si (001)-2×1 surface in atomic layer deposition (ALD) process. When H2O molecules are adsorbed on Si (001) surface at room temperature, they are dissociated with hydrogens and hydroxyls. There are two dissociation pathways; inter-dimer dissociation and intra-dimer dissociation. The activation energies of these pathways can be converted to the reaction probabilities. It was approximately 2:1. We prepared a reasonable Si substrate which consisted of six inter-dimer dissociated H2O molecules and two intra-dimer dissociated H2O molecules. The HfCl4 must react with two hydroxyls to be a bulk-like structure. There were five reaction pathways where HfCl4 could react with two hydroxyls; inter-dimer, intra-dimer, cross-dimer, inter-row, and cross-row. Inter-row, inter-dimer and intra-dimer were relatively stable among the five reaction pathways based on the energy difference. The electron densities between O and Hf in these three reactions were higher than the others and they had shorter Hf-O and O-O bond lengths than the other two reaction pathways.