Placement of quantum dots (QDs) and insight into QD's basic internal structure and optical properties lay nature cornerstones for advanced photonic devices. We report a manageable growth method for placing dense three-dimensional Ge QD arrays in a uniform or a grading size distribution, using thermal oxidation of poly-SiGe in layer-cake techniques. The QD size and spatial density in each stack could be well modulated by Ge content in poly-Si1-xGex, oxidation and underlay buffer layer conditions. Size-dependent internal structure, strain, and photoluminesce properties of Ge QDs are systematically investigated. Optimization of processing conditions was carried out for producing dense Ge QD arrays for maximizing photovoltaic efficiency.