Understanding the complex structure of polymer blends filled with nanoparticles (NPs) is key to design their macroscopic properties. Here, the spatial distribution of hydrogenated (H) and deuterated (D) polymer chains asymmetric in mass is studied by small-angle neutron scattering. Depending on the chain mass, a qualitatively new large-scale organization of poly(vinyl acetate) chains beyond the random-phase approximation is evidenced in nanocomposites with attractive polymer–silica interactions. The silica is found to systematically induce bulk segregation. Only with long H-chains, a strong scattering signature is observed in the q range of the NP size: it is the sign of interfacial isotopic enrichment, that is, of contrasted polymer shells close to the NP surface. A quantitative model describing both the bulk segregation and the interfacial gradient (over ca. 10–20 nm depending on the NP size) is developed, showing that both are of comparable strength. In all cases, NP surfaces trap the polymer blend in a non-equilibrium state, with preferential adsorption around NPs only if the chain length and isotopic preference toward the surface combine their entropic and enthalpic driving forces. This structural evidence for interfacial polymer gradients will open the road for quantitative understanding of the dynamics of many-chain nanocomposite systems.