The effect of graphene (GR) on Ni surface relaxation and reconstruction in three different substrate orientations, {111}, {001}, and {011}, at two different temperatures, 300 K and 400 K, was studied using molecular dynamics simulation. The change in the interplanar distances of the substrate and redistribution of Ni and C atoms in a direction perpendicular to the surface was compared with the equilibrium state of GR and bulk Ni, in the absence of the counterpart. The surface reconstruction for the GR/Ni system was analyzed based on the calculated radial pair distribution functions of Ni and C atoms. The surface roughness was visualized using 2D atomic distribution maps. The introduction of GR on the Ni surface in any crystallographic orientation decreases the maximum modification of interplanar spacing compared to the bulk by less than 1%. For the studied substrate orientations and temperatures, it was found that the most densely packed {111} orientation of the Ni base provides minimal changes in the structural parameters of both counterparts at 400 K. Additionally, the system formed by GR deposition on Ni {111} at 400 K is characterized by the least roughness.