An otherwise random, self-assembly of Ge/Si composite quantum dots (CQDs) on Si was controlled by inserting a layer of Si, sub-dot stacks, and post-annealing to produce micron-scale-thick QD layers with desired QD morphology, interface density, and composition distribution. A heterostructure consisting of a deliberate insertion of Si between Ge sub-dots is shown to improve the epitaxial coherence of the Ge QDs by suppression of the Ge surface interdiffusion and coarsening. As compared to regular-QD materials, the thin-film-like multifold-CQD materials are found to exhibit both reduced cross-plane thermal conductivity and enhanced electrical conductivity, and 1.5 times higher ZT value by calculation, providing a promising building block for practical thermoelectric applications in micro- or nanoelectronics.