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We have investigated in situ the morphological transformation of the Si(111) surfaces with micro-pits at large terraces during high-temperature annealing at T = 1200–1400°C. Experimental observation of the micro-pits kinetic decay have been performed by means of ultrahigh vacuum reflection electron microscopy. Focused ion beam system have been used for micro-pits creation at Si(111) terraces of large size. We have found that kinetic of micro-pit decay processes is affected by two dimensional vacancy islands nucleation at the micro-pit bottom when the micro-pit reaches the critical lateral size. The simple theoretical model has been proposed for describing the changes of the lateral size of micro-pit. The temperature dependence of two-dimensional vacancy islands nucleation frequency at micro-pit bottom is found to be described by the activation energy of 4.1 ± 0.1 eV.