•Relationship between dislocation annihilation and dislocation type is revealed.•The cause of almost no annihilation of edge dislocations is explained.•Reason for the failure of AlGaN and AlN layers to block dislocations is given. In this work, we have found that there is a clear difference between the annihilation of screw dislocation and edge dislocation, and the density of edge dislocations remains almost unchanged during the growth from AlN to GaN. Through the transmission electron microscope (TEM), the internal mechanism of this phenomenon has been explored in this paper, which can be attributed to the failure of AlGaN buffer layer and AlN insertion layer to block the edge dislocation. The explanation proposed in this paper may provide new ideas to further reduce the dislocations in GaN-on-Si, improving the crystal quality.