Fundamental understanding of macroscopic properties of polymer nanocomposites (PNCs) remains difficult due to the complex interplay of microscopic dynamics and structure, namely interfacial layer relaxations and three-dimensional nanoparticle arrangements. The effect of surface modification by alkyl methoxysilanes at different grafting densities has been studied in PNCs made of poly(2-vinylpyridine) and spherical 20 nm silica nanoparticles (NPs). The segmental dynamics has been probed by broadband dielectric spectroscopy, and the filler structure by small-angle X-ray scattering and reverse Monte Carlo simulations. By combining the particle configurations with the interfacial layer properties, it is shown how surface modification tunes the attractive polymer-particle interactions: bare NPs slow down the polymer interfacial layer dynamics over a thickness of ca. 5 nm, while grafting screens these interactions. Our analysis of interparticle spacing and segmental dynamics provides unprecedented insight into the effect of surface modification on the main characteristics of PNCs: particle interactions and polymer interfacial layers.