This study aimed to enhance the conductive properties of PLA nanocomposite by controlling the dispersion and distribution of graphene within the minor phase of the polymer blend. Functionalized graphene (f-GO) was achieved by reacting graphene oxide (GO) with various silanes under the aid of an ionic liquid. Ethylene/n-butyl acrylate/glycidyl methacrylate terpolymer elastomer (EBA-GMA) was introduced as the minor phase to tailor the interface of matrix/graphene through reactive compatibilization. GO particles were predominantly dispersed in PLA in a self-agglomerating pattern, while f-GO was preferentially located in the introduced rubber phase or at the PLA/EBA-GMA interfaces through the formation of the three-dimensional percolated structures, especially for these functionalized graphene with reactive groups. The selective localization of the f-GO also played a crucial role in stabilizing and improving the phase morphology of the PLA blend through reducing the interfacial tension between two phases. The establishment of the percolated network structures in the ternary system was responsible for the improved AC conductivity and better dielectric properties of the resulting nanocomposites.