The thickness of the optically translucent coating was evaluated using the transmission thermography. The transmitted temperature of a two-layer structure was theoretically analysed based on the equation of 1D heat transfer in the depth direction, and accordingly, the method for the measurement of coating thickness in a two-layer structure was established based on a long-pulse transmission thermography. The coating thickness was determined based on the characteristic time at the maximum half-rise temperature. Then, the proposed method was experimentally validated and calibrated by coating specimen with a different coating thickness. The thickness measurement method was further applied to measure an uneven coating specimen fabricated by mechanical grinding. The measurements were compared with a 3D digital image correlation method and the averaged relative error was less than 4%. Finally, thermal excitation, sampling rate of thermography and translucence of organic coating were discussed for accurate measurement.