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This work offers a new vision of the nanoparticle−polymer interface in inorganic nanoparticle filled thermoplastic nanocomposites in terms of macromolecular structure, conformations, and interactions. In particular, the molecular structure and interfacial conformation of PMMA in silica/PMMA nanocomposites obtained by high-energy ball milling (HEBM) have been studied. HEBM was applied to achieve an extraordinary dispersion of high content of silica nanoparticles within the PMMA polymer. Fourier transform infrared spectroscopy (FTIR) was used to investigate the effect that the important shear forces imposed by the HEBM process has on the PMMA structure and its dynamics and also the effect of the presence of silica nanoparticles inserted by HEBM on the particular conformations of PMMA appearing at the interface. It has been demonstrated that HEBM induces particular conformational changes on both the ester group and the backbone of the PMMA, which seem to be the cause of subsequent appearance of specific polymer chain packing at the interface.