A two‐stacked cubic (c‐) InN/c‐GaN nano‐scale dot structure is fabricated on a MgO(001) substrate by RF‐N2 molecular beam epitaxy and its microstructures are investigated by scanning transmission electron microscopy (STEM). The cubic lattice structure of InN dots is verified by STEM observations. It is implied that c‐InN dots formed on a smooth c‐GaN surface have the {111} facets. The c‐GaN cap layer has an uneven surface, which reflects the shape of the c‐InN dots embedded beneath the cap layer. InN selectively deposits in concave regions on the c‐GaN cap layer, which appear above in‐between positions of embedded dots. Thus, stacked c‐InN/c‐GaN dots do not tend to align vertically. These results open the possibility for multi‐stacking structures of c‐InN dots and their application to high‐performance optoelectronic devices based on the nitride semiconductors. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)