Abstract We present a theoretical-computational study of the formation, structure, composition, energetics, dynamics and expansion of nanoplasmas consisting of high-energy matter on the nanoscale of ions and electrons. Molecular dynamics simulations explored the structure and energetics of hydrogen and neon persistent nanoplasmas formed under the condition of incomplete outer ionization by the laser field. We observed a marked microscopic inhomogeneity of the structure and the charge distribution of exploding nanoplasmas on the nanoscale. This is characterized by a nearly neutral, uniform, interior domain observed for the first time, and a highly positively charged, exterior domain, with these two domains being separated by a transition domain. We established the universality of the general features of the shape of the charge distribution, as well as of the energetics and dynamics of individual ions in expanding persistent nanoplasmas containing different positive ions. The inhomogeneous three-domain shell structure of exploding nanoplasmas exerts major effects on the local ion energies, which are larger by one order of magnitude in the exterior, electron-depleted domain than in the interior, electron-rich domain, with the major contribution to the ion energies originating from electrostatic interactions. The radial structural inhomogeneity of exploding nanoplasmas bears analogy to the inhomogeneous transport regime in expanded and supercritical metals undergoing metal-nonmetal transition.