A method framework for estimating the spectral emissivity of a target is established on the basis of a Fourier Transform Infrared (FTIR) spectrometer. First, a double-temperature calibration method is used to obtain the background radiance function and responsibility function of the FTIR spectrometer, so as to improve the measurement accuracy. Secondly, high order polynomial fitting is carried out on the basis of the radiance data of the atmospheric window, so as to further suppress the interference from stray radiation. Then, by estimating the radiation characteristics at atmospheric absorption wavelengths, the infrared radiance curves in the measured wavebands are obtained. Finally, the spectral emissivity of the target is estimated. The relative error is within 1%. The measurement results show that the proposed method is effective.