Rheological behaviors of fumed silica filled hydroxylated polydimethylsiloxane suspensions were investigated in both static and dynamic shear modes. Both viscosity and modulus increase with filler’s concentration and specific surface area, however, they decrease with the improved dispersion and proper surface modification. In addition to the effective volume effect of filler’s excluded volume and polymer–filler interaction, the polymer-mediated filler–filler interaction contributes significantly. Such an interaction was classified according to the particle distance, and the concept of “inter-particle excess energy” was proposed. A combination of effective volume effect and inter-particle excess energy can be used to interpret the rheological behaviors of the nanocomposites.