Thermoelectric nanocomposites (TENCs) with inorganic nanostructures embedded in an organic matrix have attracted much attention in recent years. There is hardly any theory to guide the design of such TENC although various combinations of inorganic fillers and organic matrices are reported. We recently proposed a concept of “electron–percolation phonon–insulator” to provide a guiding ideology for designing inorganic–organic TENC. In this work, we systematically exemplify this theory by measuring the transport properties of TENC with a sequence of one-, two-, and three-dimensional nanostructured fillers embedded in an insulating poly(vinylidene fluoride) matrix. The topological structure of the connected fillers is found to be a key factor to achieve high thermoelectric performance. The intrinsic Seebeck coefficient of filler materials and the contact resistance between fillers also play important roles.