In current work, HfO2/SiO2 nanolaminates and HfO2 films were grown on AlGaN/GaN substrates via plasma-enhanced atomic layer deposition. A comparative study of how rapid thermal annealing modulates the microstructural and electrical properties of both films has been presented. It is found that the HfO2/SiO2 nanolaminate keeps an amorphous structure when thermally treated below 600 °C, whereas crystal grains appear within the 800 °C annealed sample. High-temperature annealing facilitates the transformation from Hf–O and Si–O to Hf–O–Si in the HfO2/SiO2 nanolaminates, forming an HfSiO4 composite structure simultaneously. The 800 °C annealed HfO2/SiO2 shows a low k value and large leakage current density. While the 600 °C annealed HfO2/SiO2 possesses an effective dielectric constant of 18.3, a turn-on potential of 9.0 V, as well as a leakage density of 10−2 μA/cm2 at gate biases of both −10 and 2 V, revealing good potential in fabricating high electron mobility transistors.