To enhance the bond strength of the nanosized silica/epoxy interface and modify the dielectric properties of nanocomposites, a plasma-assisted surface modification method is proposed for inorganic nanofillers. A gas–liquid two-phase dielectric barrier discharge at room temperature was initially used to graft the terminal carboxyl hyperbranched polyester onto the nanosilica surface. Then, epoxy resin composites filled with 1–7 wt. % nanosilica were prepared. The effects of the plasma-treated nanosilica on the dielectric properties of the epoxy resins were analyzed. The experimental results demonstrated that a 2 nm-thick film of hyperbranched polyester (HBP) was successfully deposited onto the nanosilica surface via the HBP/plasma treatment. Compared with the pristine epoxy resins at room temperature, the permittivity constant of the proposed nanocomposites decreased from 4.2 to 3.3 and their AC breakdown strength increased by 38%. Moreover, the dielectric loss factor and DC conductivity decreased by 40.7% and 48.4%, respectively. Additionally, deep traps of 0.99–1.53 eV were observed in the nanocomposites. It can be concluded that HBP/plasma processing creates strong chemical bonds and compact nanofiller/polymer interfacial regions. In addition, HBP/plasma processing modified the dielectric properties of the nanocomposites. The results of this study indicate that HBP/plasma treatment is an effective method for the surface modification of inorganic nanofillers and for the modification of the dielectric properties of polymer nanocomposites.