We report a simple and manageable growth method for placing dense three-dimensional Ge quantum dot (QD) arrays in a uniform or a graded size distribution, based on thermally oxidizing stacked poly-SiGe in a layer-cake technique. The QD size and spatial density in each stack can be modulated by conditions of the Ge content in poly-Si(1-x)Ge(x), oxidation, and the underlay buffer layer. Size-dependent internal structure, strain, and photoluminescence properties of Ge QDs are systematically investigated. Optimization of the processing conditions could be carried out for producing dense Ge QD arrays to maximize photovoltaic efficiency.