In this study, we investigated the growth mechanism of indium gallium nitride (InGaN) nanodots (NDs) and an InGaN layer, which were simultaneously formed on a three‐dimensional (3D) gallium nitride (GaN) structure, having (0001) polar, (11‐22) semi‐polar, and (11‐20) nonpolar facets. We observed the difference in the morphological and compositional properties of the InGaN structures. From the high resolution transmission electron microscopy (HR‐TEM) images, it can be seen that the InGaN NDs were formed only on the polar and nonpolar facets, whereas an InGaN layer was formed on the semi‐polar facet. The indium composition variation in all the InGaN structures was observed using scanning transmission electron microscopy (STEM) and the energy dispersive X‐ray spectroscopy (EDS). The different growth mechanism can be explained by two reasons: (i) The difference in the diffusivities of indium and gallium adatoms at each facet of 3D GaN structure; and (ii) the difference in the kinetic Wulff plots of polar, semi‐polar, and nonpolar GaN planes.