When the part geometry scaling down from macro to microscale level, the size-induced surface effect becomes significant in the injection molding process. The adhesion between polymer and nickel (Ni) mold insert during the process can lead to defects in necking, warping and deformation of microstructure. In this study, the self-assembled monolayers (SAMs) with low surface energy were deposited on the Ni surface to reduce the adhesion and further improve the demolding quality of the microstructure. Results show that the alkyl mercaptan SAMs with chemical bonds and close alignment can be successfully deposited on the surface of Ni by the solution deposition method. The contact angle, surface free energy, and friction coefficient before and after anti-adhesion treatment on the surface of mold insert were measured. In addition, the anti-adhesion properties of different alkyl mercaptan materials and the correspondingly replication quality of microstructure parts after injection molding were analyzed. It is found that the Ni mold insert treated by the perfluorodecanethiol has the best wear resistance and still shows good reproducibility at the 100th demolding cycle.