Recently, the significant improvements in polymer composites properties have been mainly attributed to the ability of filler nanoparticles (NPs) to self-assemble into highly anisotropic self-assembled structures. In this work, we investigate the self-assembly of core-shell NPs composed of a silica core grafted with polybutadiene (PB) chains, generating the so-called "hairy" NPs (HNPs), immersed in tetrahydrofuran solvent. While uncoated silica beads aggregate forming uniform compact structures, the presence of a PB shell affects the silica NPs organization to the point that by increasing the polymer density at the corona, they tend to self-assemble into linear chain-like structures. To reproduce the experimental observations, we propose a theoretical model for the two-body that considers the van der Waals attractive energy together with the polymer-induced repulsive steric contribution and includes an additional three-body interaction term. This term arises due to the anisotropic distribution of PB, which increases their concentration near the NPs contact region. The resulting steric repulsion experienced by a third NP approaching the dimer prevents its binding close to the dimer bond and favors the growth of chain-like structures. We find good agreement between the simulated and experimental self-assembled superstructures, confirming that this three-body steric repulsion plays a key role in determining the cluster morphology of these core-shell NPs. The model also shows that further increasing the grafting density leads to low-density gel-like open structures.