Simultaneous achievement of low thermal conductivity κ and high electrical conductivity cris a promising route for realizing Si-based thermoelectric materials. Although several attempts have been made, this requirement has still been bottlenecked by their correlated nature. In order to realize low κ and high σ simultaneously, we have proposed a nanoarchitecture that is Si films including epitaxial Ge nanodots. This nanoarchitecture was fabricated based on molecular beam epitaxy, where Ge nanodots and Si layer were stacked alternately on Si substrates using unique ultrathin SiO2 film technique. In this study, we investigated the impact of Ge nanodot incorporation and doping on the κ and σ. The κ was significantly reduced by Ge nanodot incorporation whereas the σ exhibited high value coming from Si property. This demonstrated the accomplishment of the nanostructure design for the independent control of carrier and phonon transport using the ultrasmall epitaxial Ge nanodots.