Electron-luminescence (EL) and high-resolution transmission electron microscopy (TEM) measurements have been carried out on the InGaN quantum dot (QD) based light emitting diodes (LEDs) annealed at different temperatures for p-type GaN activation. The annealing temperatures are chosen based on the growth temperature for our InGaN QDs as a reference point. A significant improvement with a factor of up to ∼3.5 in EL intensity has been achieved when the annealing temperature is increased from 720 to 800 °C. However, the EL intensity dramatically decreases if the annealing temperature further increases to 830 °C. In addition, a clear blueshift in EL emission energy has been observed as a result of increasing annealing temperature. In combination with our TEM study, the change in optical properties of the QD based LEDs due to the thermal annealing can be attributed to the shrinkage of the QDs and then eventual mergence into the wetting layer if the annealing temperature is further increased. The data based on detailed driving-current dependent EL measurements also support the conclusion.