Simplified silica (Zeosil 1165 MP) and SBR (140k carrying silanol end-groups) nanocomposites have been formulated by mixing of a reduced number of ingredients with respect to industrial applications. The thermo-mechanical history of the samples during the mixing process was monitored and adjusted to identical final temperatures. The filler structure on large scales up to micrometers was studied by transmission electron microscopy (TEM) and very small-angle X-ray scattering (SAXS). A complete quantitative model extending from the primary silica nanoparticle (of radius ≈10 nm), to nanoparticles aggregates, up to micrometer-sized branches with typical lateral dimension of 150 nm is proposed. Image analysis of the TEM-pictures yields the fraction of zones of pure polymer, which extend between the branches of a large-scale filler network. This network is compatible with a fractal of average dimension 2.4 as measured by scattering. On smaller length scales, inside the branches, small silica aggregates are present. Their average radius has been deduced from a Kratky analysis, and it ranges between 35 and 40 nm for all silica fractions investigated here (Φsi = 8−21% vol.). A central piece of our analysis is the description of the interaggregate interaction by a simulated structure factor for polydisperse spheres representing aggregates. A polydispersity of 30% in aggregate size is assumed, and interactions between these aggregates are described with a hard core repulsive potential. The same distribution in size is used to evaluate the polydisperse form factor. Comparison with the experimental intensity leads to the determination of the average aggregate compacity (assumed identical for all aggregates in the distribution, between 31% and 38% depending on Φsi), and thus aggregation number (ca. 45, with a large spread). Because of the effect of aggregate compacity and of pure polymer zones, the volume fraction of aggregates is higher in the branches than Φsi. The repulsion between aggregates has a strong effect on the apparent isothermal compressibility: it leads to a characteristic low-q depression, which cannot be interpreted as aggregate mass decrease in our data. In addition, the reinforcement effect of these silica structures in the SBR-matrix is characterized with oscillatory shear and described with a model based on the same aggregate compacity. Finally, our results show that it is possible to analyze the complex structure of interacting aggregates in nanocomposites of industrial origin in a self-consistent and quantitative manner.