Hydrogen ion implantation in aluminium nitride (AlN) epitaxial layers grown on 2-inch c-plane (0001) sapphire substrates was performed with different fluences in the range of 1 × 1017–2 × 1017/cm2 at various implantation temperatures between liquid nitrogen (LN2) to 300 °C. The post-implantation thermal annealing behaviour of these samples was studied by using optical microscopy, atomic force microscopy (AFM) and transmission electron microscopy (TEM). Our investigations showed that AlN samples that were implanted at LN2 and room temperature (RT) exhibited mostly surface blistering after post-implantation annealing. On the other hand, the AlN samples that were implanted at 100 and 300 °C showed large area exfoliation of the implanted surface after post-implantation annealing. The implantation-induced damage in AlN was analysed by cross-sectional TEM, which revealed a damage band inside the AlN layer in all the cases that was decorated with hydrogen-filled nanovoids. These nanovoids showed a greater tendency of agglomerating together to form nanocracks in the as-implanted state for 100 and 300 °C implanted samples leading eventually to the large area exfoliation after high temperature annealing.