This study investigates the thermal decomposition behavior of GaN-based epilayers on patterned sapphire substrates (GaN-epi/PSSs) in a quartz furnace tube under a hydrogen atmosphere. The GaN-epi/PSS was decomposed under different hydrogen flow rates at 1200 °C, confirming that the hydrogen flow rate influences the decomposition reaction of the GaN-based epilayer. The GaN was completely removed and the thermal decomposition process yielded gallium oxyhydroxide (GaO2H) nanostructures. When observed by transmission electron microscopy (TEM), the GaO2H nanostructures appeared as aggregates of many nanograins sized 2–5 nm. The orientation relationship, microstructure, and formation mechanism of the GaO2H nanostructures were also investigated.