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Theoretical studies of the properties of the interface between the polymer matrix and surface-modified nanoparticles encounter a lot of problems which are caused by the need to take into account many parameters simultaneously. Nevertheless, the large body of facts accumulated recently makes it possible to consider the problem of studying ultrathin polymer films in a direct connection with the research of nanocomposite materials. This analogy is explained by the large contribution of the matrix located in the range of surface forces in the case of both ultrathin films and filled polymers. In this work, we studied the effect of the surface density and molecular weight of a modifier on the properties of a polymer–nanoparticle interface in the frame of atomistic simulation. The model of polyimide–SiO2 nanocomposite was constructed as alternate layers of polymer matrix and inorganic substrate, which may be considered on account of the above analogy. As a matrix we used a polyimide obtained from two monomers: 3,3',4,4'-biphenyltetracarboxylic dianhydride and 1,3-bis(4-aminophenoxy) benzene. For the sake of simplicity, the model of the substrate was built assuming a unit cell of silicon dioxide (in the crystalline form of β-cristobalite) as an infinite layer. Alkylsilyl molecules and hydroxyl groups were used as surface modifiers.