Taking the Poiseuille flow of a molten polymer in parallel plates as the research object and polymethyl methacrylate (PMMA) as the research material, an all-atom analysis model of the molecular dynamic flow of polymer macromolecules is established according to the Navier slip law. The effects of wall wettability and external pressure on the wall slip behaviour of polymer macromolecules, as well as the spatial evolution process of the entanglement–unentanglement process of polymer chains near the wall under different shearing effects, were studied. The interface thermal resistance rule was explored, and an interface thermal resistance model considering the wall slip behaviour was established. Finally, a micro-injection experiment was used to verify the validity and accuracy of the model. The results show that when the wall is hydrophobic, the polymer melt exhibits significant wall slip. As the external pressure increases, the wall slip speed and the slip length increase. However, after a certain pressure is exceeded, the growth rate of the slip length is basically zero. As the external pressure increases, the PMMA molecular chains gradually start to separate, the single molecular chain becomes untangled from the entangled grid, and the chain detaches from the wall after exceeding a certain threshold. Wall slip reduces the interface thermal resistance between the solid–liquid interface and enhances the interface heat transfer performance. The interface thermal resistance value calculated by molecular dynamics can more accurately reflect the heat conduction rule of the solid–liquid interface at the micro/nanoscale than that measured by the thermal resistance experiment, indicating that the micro/nano interface thermal resistance obtained by molecular dynamics simulation is reliable.