A graphene aerogel cross-linked by p-phenylenediamine (PPDA) composite with Sm2O3 nanoparticles (AP.Sm) was synthesized as a novel nanocomposite via a one-step hydrothermal method. PPDA, as a spacer, provided a large surface area by reducing the adhesion of graphene ultrathin sheets. It also functioned as a source of nitrogen. Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) were performed for structural characterization. The resulting nanocomposite was then investigated for its supercapacitive behavior using electrochemical techniques. As the results confirmed, the cross-linked structure of the nanocomposite effectively promoted its supercapacitive function at 6 M KOH. The specific capacitance of the nanocomposite electrode reached 591 F/g at 5 mV/s, and decreased by only 7.3% after 4000 cyclic voltammetry (CV) cycles. The AP.Sm electrode increased the energy density to as high as 55 Wh/Kg. Owing to its unique structure, the fabricated aerogel can be recommended for broad use in numerous applications. In addition, theoretical calculations for the graphene oxide (GO) and modified GO structure and frontier molecular orbital (FMO) analysis was carried out using the Austin Model 1 (AM1) method and density functional of theory (DFT). The calculated HOMO–LUMO energy gap and thermochemical energies indicated good agreement with the experimentally investigated data for compounds.