The influence of surface-modification of TiO2-nanoparticles with phosphonic acid molecules on the structure of polymer nanocomposites has been studied by small-angle scattering and transmission electron microscopy. The grafting of phosphonic acids was done by phase transfer into chloroform, and polymer nanocomposites have been formulated by solvent casting with two polymers of slightly different hydrophobicity, PMMA and PEMA. By analyzing the shape of the scattering curves around the interparticle correlation peak, and in particular the depth of the correlation hole, information on nearest neighbor correlations between nanoparticles is obtained. While local nanoparticle arrangements are found to be independent of the global particle volume fraction, they are controlled by the degree of hydrophobicity of the alkyl phosphonic acid grafts with respect to hydrophobicity of matrix. Quantitative analysis of the correlation hole thus evidences the fine-tuning of local nanocomposite structure with phosphonic acids.