Using molecular dynamics (MD) simulations, the defect evolution and plastic deformation mechanism of single-crystalline and polycrystalline copper under spherical nanoindentation are investigated and compared with previous nanoindentation simulations and experiments. To reveal the grain size effects on the indentation-induced internal stress and deformation behavior, the polycrystalline copper with different grain size are adopted in nanoindentation simulations, whose grain size are follow the inverse Hall-Petch relation. To study the grain boundary network effect, the grain boundary interface is further divided into three microstructural components with different dimensions. The results show that the indentation force of single-crystalline copper is larger than that of polycrystalline copper, and that of polycrystalline copper continuously decreases with the decrease of grain size due to softening phenomenon. The defect nucleation and propagation region in both single-crystalline and polycrystalline copper appear below the tool tip, due to the high internal stress and atomic potential energy induced by nanoindentation. The horizontal propagation of defects is faster and larger than the vertical propagation of that, and such defects are limited in the grains around the tool tip due to grain boundary network. An obvious stresses and potential energy gradient exist under tool tip in single-crystalline copper, and such gradients are possibly distributed along multiply direction in the polycrystalline copper. The internal stresses and atomic potential energy in the region of VP are highest, followed by that in TJ, GB and VP, resulting in the defect nucleation and propagation are more possible occur in VP than other microstructural components.