A comprehensive understanding of the adhesive characteristics and molecular kinetic mechanisms of heterogeneous composite materials is of great significance for promoting nanotechnology applications. Polybutylene terephthalate (PBT), aluminum (Al), iron (Fe), 2-amino-1,3,5-triazine-4,6-dithiol (ATD), and the oligomer of three ATDs (3ATDs) were selected as experimental materials. This work established six polymer−substrate interface models with a conical nanoslot. Comprehensive simulations from molding to failure processes were conducted by molecular dynamics. The results indicated that the polymer filled the substrate with a migration-type anchor through wall slip in the models without ATD/3ATDs coatings, while other models with coatings exhibited restricted anchor slip behavior. The shear behavior of chains at the interface showed a greater contribution from restricted anchor when the shear stress was kept within the anchoring threshold. As the stress increased, the chain segments exhibited migration anchor behavior. When the polymer−substrate interface underwent shear failure, the polymer material section above the heterogeneous interface was preferentially damaged. Heterogeneous interfaces were not prone to tearing, but internal defects in the polymer layers were often preferentially damaged. The Fe with BCC crystal lattice was more suitable for nanoinjection molding than the Al with FCC. Coatings such as ATD/3ATDs contributed positively to the nanoinjection molding and all-directional resistance in failure damage.