Polypropylene (PP) multilayer films were prepared by novel microlayer coextrusion technology. Molecular dynamics simulations were carried out to investigate the effect of multilayer nanostructures on the barrier properties of PP films from the perspective of microscopic molecular chain orientation. The experiments suggest that, compared with PP monolayer films, the barrier properties of PP multilayer films are significantly improved, with oxygen and water vapor transmission coefficients decreased by 23.9% and 86.4%, respectively. In order to explore the barrier properties of PP multilayer films from the perspective of microstructure, the permeability models of PP monolayer and multilayer films were investigated by molecular dynamics simulations. The small molecule diffusion paths through PP monolayer and multilayer films were compared using permeability models. The two-dimensional molecular chain orientation at the interface of PP multilayer films makes the small molecule diffusion paths more tortuous compared to those of PP monolayer films. This is one of the important reasons for the excellent barrier properties of PP multilayer films. Simultaneously, the accuracy of the permeability models was verified by comparative experimental analysis between mechanical properties of PP monolayer and multilayer films.