Various nanostructured amorphous silicas [fumed silicas such as crude (A-300), hydro-compacted (cA-300, TS 100), and precipitated silica Syloid 244] were modified by different polydimethylsiloxanes such as PDMS5, PDMS100, PDMS200, PDMS1000, and PDMS12500 (the label numbers show the viscosity (η) values) using dimethyl carbonate (DMC) as a siloxane-bond-breaking reagent. In addition, hexamethyldisilazane was used to modify fumed silica cA-300. The nanocomposites were characterized using microscopy, infrared spectroscopy, thermodesorption, nitrogen adsorption-desorption, solid-state NMR spectroscopy, small-angle X-ray scattering, and zeta-potential methods. It was found that the morphological, textural, and structural characteristics of silicas grafted with PDMS depend strongly not only on the type and content of the polymers used but also on the organization of nonporous nanoparticles (NPNP) in secondary structures (aggregates of NPNP and agglomerated aggregates, ANPNP), as well on the reaction temperature (T r). Specifically, we determined that ANPNP with a macro/mesoporous character are favorable for the effective modification of the silicas studied with short polymers and no DMC addition but at higher temperatures or for a longer silicone polymer with the presence of DMC and at lower temperatures. In particular, the PDMS/DMC-modified silicas are of great interest from a practical point of view because they remain in a dispersed state with no strong compaction of the secondary structures after modification, and this corresponds to a better distribution of the modified nanoparticles in polymeric or other matrices.