To study the effect of microstructural components on the mechanical properties and deformation mechanism of polycrystalline copper during the nanoindentation process, a large-scale molecular dynamics simulation model of polycrystalline copper is structured by Poisson-Voronoi method and Monte Carlo method. Based on the microstructural components of the nanocrystalline copper, the polycrystalline copper nanoindentation simulation models with initial nanoindentation position at different microstructural components that contain grain cell, grain boundary, triple junction and vertex points are established, respectively. The nanoindentation process with the four different initial nanoindentation positions are simulated by molecular dynamics method, and the nanoindentation force and internal stress of the microstructural components are calculated. Centrally symmetric parameter method is used to analyze the dislocation nucleation and propagation process in the surface and subsurface of the polycrystalline copper with different initial nanoindentation positions. The results show that there is obvious regularity of the microstructural components during the nanoindentation process: the nanoindentation force rate, the difficulty of dislocation propagate to adjacent grains, the size expansion of dislocation distribution range on the polycrystalline surfaces, as well as the ability of the microstructural component low dimension accumulating atomic potential energy satisfy the descending relationship: grain cell, grain boundary, triple junction and vertex points. In addition, when the indentation position is at the high-dimensional microstructural component, the adjacent microstructural component exhibits tensile stress, while the indentation position is at the low-dimensional microstructural component, the adjacent microstructural component exhibits compressive stress. Therefore, during the nanoindentation process of polycrystalline copper, it is suggested to machine the microstructural components like grain cells of the polycrystalline material and to avoid the microstructural components like vertex points and triple junctions to reduce the number and energy accumulation of dislocations and the residual stress in the workpiece.