We demonstrate a GaN/AlGaN photonic crystal thermal emitter supported by a semi-transparent low-refractive-index substrate for mid-wavelength infrared operation. The employment of the substrate increases the mechanical strength of the photonic crystal, and enables the fabrication of a large-area thermal emitter for high power operation. First, we numerically investigate the control of emission spectra of the GaN/AlGaN photonic crystal thermal emitters and found that nearly single-peak emission in the normal direction can be realized in spite of the lower and asymmetric refractive index contrast due to the existence of the substrate. Then we fabricate a GaN/AlGaN thermal emitter with an area of 3.4 mm × 3.4 mm on a sapphire substrate, and experimentally demonstrate narrowband thermal emission with a Q factor of 101 and an emission power of 25 mW/μm/sr at 800°C.