A film growth of a virtual GdCo amorphous binary alloy was studied with a molecular dynamics simulation. A deviation of the atomic environment δ and an atomic pair distribution index η were calculated to evaluate the atomic structure of the prepared film. It was found that an anisotropic atomic distribution is induced in the film. The value of δ for a Gd atom environment is of the order of 10−4 and is almost in quantitatively agreement with the experimental value. The anelastic deformation is affected by the roughness of the substrate and becomes large in the film deposited on a smooth substrate. The value of η shows that the atomic pairs preferentially orient toward a horizontal film plane. The obtained results strongly support a single ion model as a main origin of a perpendicular magnetic anisotropy experimentally observed in amorphous rare earth-transition metal alloy films.