In micro-injection molding, the interaction between the polymer and the mold insert has an important effect on demolding quality of nanostructure. An all-atom molecular dynamics simulation method was performed to study the effect of nanostructure shape, interfacial adhesion energy, and mold insert material on demolding quality of nanostructures. The deformation behaviors of nanostructures were analyzed by calculating the non-bonded interaction energies, the density distributions, the radii of gyration, the potential energies, and the snapshots of the demolding stage. The nanostructure shape had a direct impact on demolding quality. When the contact areas were the same, the nanostructure shape did not affect the non-bonded interaction energy at PP-Ni interface. During the demolding process, the radii of gyration of molecular chains were greatly increased, and the overall density was decreased significantly. After assuming that the mold insert surface was coated with an anti-stick coating, the surface burrs, the necking, and the stretching of nanostructures were significantly reduced after demolding. The deformation of nanostructures in the Ni and Cu mold inserts were more serious than that of the Al2O3 and Si mold inserts. In general, this study would provide theoretical guidance for the design of nanostructure shape and the selection of mold insert material.