We study nuclear symmetry energy of dense matter using holographic QCD. We calculate it in a various holographic QCD models and show that the scaling index of the symmetry energy in dense medium is almost invariant under the smooth deformation of the metric as well as the embedding shape of the probe brane. We find that the scaling index depends only on the dimensionality of the branes and space-time. Therefore the scaling index of the symmetry energy characterizes the universality classes of holographic QCD models. We suggest that the scaling index might be also related to the non-fermi liquid behavior of the interacting nucleons.