The quantum-dot samples with single Ge layer and twofold stacked Ge layers are prepared by ion beam sputtering deposition. The different sizes and morphologies of quantum-dots are characterized using atomic force microscope technique. The effects of strain from the capped Ge quantum-dots on the upper Ge wetting layer and the nucleation are also investigated by the buried strain model. The results show that the non-uniform strain in the Si spacing layer which caps the buried quantum-dot layer, leads to the decrease of Ge critical thickness in the upper layer, which increases the upper dot size. The strain intensity increases with the decrease of Si spacer thickness, which results in the changes of dot shape and size in the upper layer. Furthermore, the strain also modulates the distribution of upper quantum-dot layer.