We have investigated the spatial evolution of (n×3) surface reconstructed areas during the molecular beam epitaxial growth of InAs–GaAs(001) by using ab initio-based calculation and in situ observation, in order to understand the mechanism of consequent QD nucleation. Statistical analysis of (n×3)-reconstructed morphology reveals that the fraction of (8×3)-reconstructed areas, as well as those of (4×3) and (6×3), appears and decreases in the later stage of the growth. This behaviour is consistent with the result of our ab initio-based calculation incorporating chemical potentials of source materials in the gas phase. In contrast, fragmented (2×3) areas remain throughout the InAs growth as potential QD nucleation sites.