The high electrical and drastically-low thermal conductivities, a vital goal for high performance thermoelectric (TE) materials, are achieved in Si-based nanoarchitecture composed of Si channel layers and epitaxial Ge nanodots (NDs) with ultrahigh areal density (~10(12) cm(-2)). In this nanoarchitecture, the ultrasmall NDs and Si channel layers play roles of phonon scattering sources and electrical conduction channels, respectively. Electron conductivity in n-type nanoacrhitecture shows high values comparable to those of epitaxial Si films despite the existence of epitaxial NDs. This is because Ge NDs mainly scattered not electrons but phonons selectively, which could be attributed to the small conduction band offset at the epitaxially-grown Si/Ge interface and high transmission probability through stacking faults. These results demonstrate an independent control of thermal and electrical conduction for phonon-glass electron-crystal TE materials by nanostructure designing and the energetic and structural interface control.