Polymer-metal hybrid structures have been increasingly used to replace metallic components. Direct injection joining is one of the most promising technologies in fabricating polymer-metal hybrid structure. In this study, molecular dynamics method was used to study the interfacial interaction and joining property. Interfacial models with different surface structures on aluminum (Al) substrate were constructed. The influences of surface structure, non-bonded interaction strength, and pull-out force during the separation were systematically explored. Simulation results show that an obvious difference in polymer structure along z-axis is observed during the joining process. Influenced by the interfacial interaction, the atomic density is at its largest near the interface. As the separation continues, growing voids are observed near the interface. Polymer chains close to the Al substrate are greatly stretched, while the chains far away from the interface are relatively steady. Nevertheless, the changes in radius of gyration during the separation are much higher regardless of the substrate structures. The contact area mainly contributes to the interaction energy, whereas the mechanical interlocking formed in the undercut area contributes to the maximum inner force and work of separation. Moreover, the interfacial interaction is also affected by the non-bonded interaction strength and the pull-out force.