Molecular dynamics (MD) simulations are applied to elucidate the anisotropic characteristics in the material responses for crystallographic nickel substrates with (100), (110) and (111) surface orientations during nanoindentation, compensating for the experimental limitation of nanoindentation—particularly for pure nickel substrates of three crystallographic orientations. This study examines several factors under indentation: three-dimensional phases of plastic deformation which correspond to atomic stress distributions, pile-up patterns at maximum indentation depth, and extracted material properties at different crystallographic orientations. The present results reveal that the strain energy of the substrate exerted by the tip is stored by the formation of the homogeneous nucleation, and is dissipated by the dislocation sliding of the {111} plane. The steep variations of the indentation curve from the local peak to the local minimums are affected by the numbers of slip angle of {111} sliding plane. The pile-up patterns of the three nickel substrates prove that the crystalline nickel materials demonstrate the pile-up phenomenon from nanoindentation on the nano-scale. The three crystallographic nickel substrates exhibit differing amounts of pile-up dislocation spreading at different crystallographic orientations. Finally, the effects of surface orientation in material properties of FCC nickel material on the nano-scale are observable through the slip angle numbers of {111} sliding planes which influence hardness values, as well as the cohesive energy of different crystallographic surfaces that indicate Young's modulus.