Understanding the effects of the molecular weight of the polymers and the pore size of the adherend surface on the mechanical interlocking of polymer/substrate interfaces is central for enhancing the corresponding adhesion strength. In the present study, we comprehensively investigated the effects of the molecular weight of polybutylene terephthalate and the nanostructure size on the replication quality by molecular dynamics simulations. Under practical pressures and temperatures, polymers of various molecular weights infiltrated to the bottom of the nanopores; the filling rate was > 90 %. The high filling rate and infiltration depth were attributable to the large external pressure (which can overcome the increased viscosity) and the semi-spherical nature of the nanopores (beneficial for polymer infiltration). The nanostructure size weakly corresponded to the filling rate and interfacial energy, but substantially affected the infiltration of the polymer chains. The entanglements of long-chain polymers remained during the filling and increased the joint strength, by enhancing the internal friction and the interfacial friction between the polymer and copper substrate. The current findings provide new insights into the effects of the nanostructure size and the molecular weight of the polymer on the replication quality of nanoinjection molding.