By combining state-of-the-art microscopy, spectrosccopy, and first-principles calculations, atomic-scale intermixing behavior at heterointerfaces in SrTiO3-based superlattices is investigated. It is found that Nb is confined to a unit-cell thickness without intermixing, whereas Ba diffuses only to the adjoining Nb-doped SrTiO3 layer. It is revealed that the intermixing behaviors at the heterointerfaces are determined by not only the migration energy, but also by the vacancy-formation energy and the Fermi energy of each layer. Based on these results, we find a method to control the atomic-scale intermixing at the nonpolar heterointerfaces and clearly demonstrate the property improvements obtained by constructing an abrupt heterointerface.