Flame temperature, which is an important parameter in combustion diagnostics, provides a better understanding of flame radiative characteristics and can be deduced from the flame emission spectrum. However, in a combustion process with a large-scale flame that requires field measurement, considerable attenuation of the signature from the flame source occurs owing to the absorption of cold molecules in the atmosphere, which produces uncertainties while estimating the flame temperature. We analyze the effect of atmospheric absorption on the flame temperature estimation uncertainty with the optical emission spectroscopic method. We determine the flame temperature of IR (infrared) countermeasure flare combustion by fitting the reference spectrum model applying atmospheric absorption and without applying atmospheric absorption. Line-by-line modeling is conducted using a high-temperature molecular spectroscopic database. The instrument function of the spectrometer is applied, and the atmospheric transmission information is obtained by using the moderate-resolution atmospheric transmission database. In addition, we calculate the estimated flame temperature uncertainty without applying atmospheric absorption when the atmospheric path length, molecular concentration, and flame temperature are varied. Through the analysis, we suggest the wavelength range where the atmospheric absorption is negligible so that the uncertainty is minimized without applying it. Finally, we determine the flame temperature of the IR flare detected with an absolutely calibrated radiometric spectrometer by considering atmospheric absorption. All the fitting results show good agreement with experimental data.