Four interfacial models, including the PBT-Al&P (Plane), PBT-Al&V (V-slot), PBT-ATD-Al&P (Plane), and PBT-ATD-Al&V (V-slot), were constructed. The molecular dynamics (MD) method was launched to study the interfacial interactions and bonding behaviors between heterogeneous interfaces in nano-injection molding. The influence mechanism of the 2-amino-1,3,5-triazine-4,6-dithiol (ATD) coating on adhesion properties of the PBT–Al interface was mainly explored. Results indicated that the nano-V-slot interface system exhibited a double-wall-slipping phenomenon, unlike the non-nano-interface (macroscale molding) one. In nano-V-slot interfacial models, although the ATD coating reduced the double-wall-slipping velocity, it also increased the polar bonding, thus strengthened a better anchoring connection in the PBT–ATD–Al interface. The addition of the ATD layer did not cause chemical bonding of the original PBT materials; the interlocking effect behavior occurred between them and only coexisted in the form of physical anchors. Whatever model it was, the ATD layer interface had significantly higher interface energy than the other one, which was formed solely by PBT and Al substrate. In nano-injection molding, when the ATD intermediate layer was added, the bonding behavior of the PBT–Al interface also changed from simple nonbonded rigid anchoring to the entanglement anchor between the PBT–ATD macrochains and the nonbonding connections between ATD-Al interfaces.