An epitaxial NiSi structure on Si (001) substrate was studied by using density functional theory (DFT). Orhorhombic and B2-NiSi structures were compared first. B2 structure was further considered as it has same crystal structure as Si and the lattice mismatch between B2 and Si is small, compared to orthorhombic-NiSi. The lattice parameters of x- and y-direction in B2-NiSi structure were modified to match with those in Si (001). The size reduction of the lattice parameter of B2-NiSi to match with that of Si increased the lattice parameter of z-direction by 10.5%. Therefore, we propose that an optimum structure of NiSi for epitaxial growth on Si (001) is a tetragonal structure.