In this work, GaN layer was deposited on patterned sapphire substrate (PSS) by e-beam evaporator and subsequently subjected to ammonia annealing at different temperatures of 900 °C, 950 °C, 980 °C and 1100 °C. The crystalline properties of the GaN layer improved as the temperature increased. In particular, the crystalline grains of the layer were transformed into more distinguishable structures and bigger size by increasing the annealing temperature. However, the unwanted Ga2O3 inclusions also presented in the layer due to the oxygen incorporation during the deposition. Such inclusions can be significantly suppressed by annealing the GaN layer at 980 °C. On the other hand, the re-evaporation of nitrogen atoms from the GaN layer became important at 1100 °C. Therefore, the oxygen from the annealing environment incorporated into the layer and formed the Ga2O3 inclusions.