A strong topographical evidence of the 2D to 3D transition in InAs/GaAs nanostructures assembled by the submonolayer (SML) growth mode using molecular beam epitaxy (MBE) is reported. Whereas the 2D to 3D transition in InAs nanostructures assembled by the Stranski–Krastanov (SK) growth mode is well established with a critical thickness of around 1.7 monolayer (ML), the analogous phenomenon in SML‐grown nanostructures is not yet well understood. Herein, atomic force microscopy (AFM) is utilized to investigate the topographical changes associated with the 2D to 3D transition in SML nanostructures, and it is unambiguously shown that for a given number of stacks and GaAs matrix (spacer) layer thickness, there exists a critical thickness in the amount of deposited InAs per cycle, beyond which the nucleation of 3D nanostructures abruptly begins. It is also shown that the critical thickness decreases with increasing number of stacks as well as with decreasing GaAs matrix layer thickness. Moreover, the present work shows that InAs/GaAs SML nanostructures exist in two distinct forms: 2D wetting layer (WL)‐like islands and 3D quantum dot (QD)‐like structures.