The action range of airborne infrared search and track (IRST) system is affected by the large humidity of atmosphere in low latitude areas. Aiming at this problem, the main factors affecting the atmospheric transmittance are analyzed based on the atmospheric data in low latitude areas in recent years. The mathematical model of atmospheric transmittance is established. The impact of height and oblique distance are also revised. Atmosphere transmittance at the wave band from 3 μm to 5 μm is analyzed by using Matlab under different seasons, weather conditions, pitching angles, heights and distances. Comparing with the simulation results of LOWTRAN7, the error is about 5%, which verifies the effectiveness of the model. The conclusion has significant reference value on guiding the practical operation of IRST system.