The paper presents an effect of mild annealing treatments on structural ordering and open edge morphology of graphite nanoflakes (GNF). Thin graphite flakes were obtained from the bulk highly oriented pyrolytic graphite by a prolonged grinding in a pure argon atmosphere and were annealed at T = 670 K for 24 h either in vacuum or in the air. Modification of GNF open edges was studied with high-resolution transmission electron microscopy (HRTEM) and 2D-Fourier analysis of the open edge area HRTEM-images. The morphology of the GNF edges evolve differently under annealing, revealing itself in the azimuthal width of the two-dimensional fast-Fourier transform (2D-FFT) maxima. After annealing in the air, the width decreased, while the vacuum treatment lead to its growth. We relate the former to the open edge flattening via removal of the edge defects by transformation to the gaseous carbon oxides, the latter – to the opposite process of defect accumulation in vacuum with the transformation of the near-edge structure to the less ordered one. The correlation is found between the intensity of the (101) powder X-ray diffraction maximum and the azimuthal width of the FFT-peaks indicating the direct relation of these quantities.