The apparent temperature errors caused by emissivity indexes of 940 nm monochromatic thermometry, 1550 nm monochromatic thermometry and 940 nm/1550 nm colorimetric thermometry and deviation between the actual temperatures and apparent temperatures are theoretically compared based on infrared thermometry principle, film equal thickness interference model and relative optical properties. These are conducted during preparation of 10 μm GaN epitaxy wafer on Al2O3, SiC and Si by using metal-organic chemical vapor deposition (MOCVD) technique. Moreover, the results of 940 nm monochromatic thermometry and 940 nm/1550 nm colorimetric thermometry of the blue light emitting diode (LED) epitaxial wafer with InGaN/GaN multiple quantum wells (MQW) structure growing on silicon (111) substrate verify the correctness of the modeling and the computation. The study result shows that the distinction of apparent temperature error coefficients with the same thermometry on different substrates is small in the range from 500 ℃ to 1300 ℃. The error coefficient with the same substrates from small to large are colorimetric thermometry, 940 nm monochromatic thermometry and 1550 nm monochromatic thermometry. Deviation between the actual temperatures and apparent temperatures on the different substrates with the same thermometry is large. The deviation with the same substrates from small to large are colorimetric thermometry, 1550 nm monochromatic thermometry and 940 nm monochromatic thermometry. This computational method and conclusion can be used for reference to develop the infrared thermometry device and choose the thermometry of the GaN epitaxy on different substrates.