The microstructure of polymer nanocomposites made with disordered silica filler (Zeosil(R) 1165MP) of industrial relevance and various coating agents is quantitatively analyzed using a combination of SAXS, TEM, and a recently developed structural model. The polymer matrix is formed by an endfunctionalized styrene-butadiene statistical copolymer capable of covalent grafting on the silica nanoparticles. The effect of the coating agents with different alkyl chain length (C 8 , C 12 , and C 18 ) on filler structure quantified in terms of aggregate formation, for different concentrations (up to 8%wt with respect to silica), and the effect of a commonly added catalyzer, DPG, are studied using the structural model. As a result we show that a strongly synergetic effect of both DPG and coating agent exist. Our findings open the road to a fundamental understanding and rational design of model and industrial nanocomposite formulation with optimized coating agents.