Heterogeneous nucleation plays an important part in the solidification process. In order to describe the effects of the substrate surface on the heterogeneous nucleation, an idealized planar interface between the nucleus and the substrate is assumed in the consideration of the classical nucleation theory, but this may lead to the deviation of the experimental results from the theoretical predictions, since there is no idealized planar surface on any actual substrate. The heterogeneous nucleation procedure of solid phase on rough substrate surface is investigated, and the effect of the roughness factor of the substrate on nucleation energy is analyzed based on the Wenzel wetting model. The results show that when the intrinsic contact angle between the substrate and the nucleus in the base phase is less than 90°, higher roughness of the substrate surface makes it easier to induce heterogeneous nucleation; when intrinsic contact angle is greater than 90°, higher roughness would restrict the nucleation on the substrate surface. Meanwhile, attaching and wetting drift embryos on the substrate play an important part in the formation of effective nucleus on the substrate, while the change of interfacial free energy in the wetting process of the embryos on the rough substrate surface has an important effect on heterogeneous nucleation behaviors.