Due to the adhesion between the polymer melt and nickel (Ni) mold insert in the micro injection molding process, deformation defects frequently occur when the microstructures are demolded from the insert. In this study, self-assembled alkanethiols were applied to modify the surface of Ni mold insert to reduce its surface energy. Experimental trials were undertaken to explore the effect of alkanethiols coating on the replication quality. After that, molecular dynamics (MD) simulation was then used to investigate the adhesion behavior between the self-assembled coating and polypropylene (PP) by establishing three different types of alkanethiol material. The interaction energy, the potential energy change and radial distribution function were calculated to study the anti-adhesion mechanism. Experimental results show that all the three coatings can effectively decrease the adhesion and therefore promote the replication fidelity. It is demonstrated in MD simulation that the adhesion mainly comes from the van der Waals (vdW) force at the interface. The arrangement of sulfur atom on the Ni surface results in different absorbing behaviors. Compared with that of the PP–Ni interface, the interfacial energy and adhesion work after surface treatment is significantly reduced.