The structure of silica-latex nanocomposites of three matrix chain masses (20, 50, and 160 kg/mol of poly(ethyl methacrylate)) are studied using a SAXS/TEM approach, coupled via Monte Carlo simulations of scattering of fully polydisperse silica nanoparticle aggregates. At low silica concentrations (1 vol. %), the impact of the matrix chain mass on the structure is quantified in terms of the aggregation number distribution function, highest mass leading to individual dispersion, whereas the lower masses favor the formation of small aggregates. Both simulations for SAXS and TEM give compatible aggregate compacities around 10 vol. %, indicating that the construction algorithm for aggregates is realistic. Our results on structure are rationalized in terms of the critical collision time between nanoparticles due to diffusion in viscous matrices. At higher concentrations, aggregates overlap and form a percolated network, with a smaller and lighter mesh in the presence of high mass polymers. The linear rheology is investigated with oscillatory shear experiments. It shows a feature related to the silica structure at low frequencies, the amplitude of which can be described by two power laws separated by the percolation threshold of aggregates.