Profile imaging by in situ high-resolution transmission electron microscopy is used to elucidate reconstructions of the GaN(0 0 0 -1) surface during annealing in the TEM. We have successfully captured a detailed process of a change from the stacking sequence of the wurtzite to that of the zincblende structure in the topmost three Ga layers for the surface with nanoscale hill-and-valley structures. For ab initio calculations of the change in the sequence, a model structure is approximated by the addition of a 1 × 1 Ga layer on the GaN(0 0 0 -1) surface (i.e., 1 × 1 Ga-adlayer structure). The ab initio calculations predict that, as the surface size decreases, the 1 × 1 Ga-adlayer structure with the wurtzite stacking sequence in the topmost three Ga layers becomes destabilized against the adlayer with the zincblende stacking sequence in the surface layers, which well elucidates the experimental observation.