Polymer-based nanocomposites properties are greatly affected by interfacial interaction. Polyacrylate nanocomposites have been widely studied, but few studies have been conducted on their interface mechanism. Therefore, there was an urgent demand for providing a thorough understanding of the polymethyl acrylate/SiO2 (PMA/SiO2) nanocomposites to obtain the desired macro-performance. In this paper, a methodology, which combined molecular dynamics simulation with experimental researches, was established to expound the effect of the surface structure of SiO2 particles which were treated with KH550, KH560 or KH570 (KH550-SiO2, KH560-SiO2 and KH570-SiO2) on the mechanical characteristic and water vapor permeability of polymethyl acrylate/SiO2 nanocomposites. The polymethyl acrylate/SiO2 nanocomposites were analyzed in binding energy and mean square displacement. The results indicate that PMA/KH570-SiO2 had the highest tensile strength, while PMA/KH550-SiO2 had the highest elongation at break at the same filler content; KH550-SiO2 spheres can significantly improve water vapor permeability of polyacrylate film.