The windows of IR detection systems becomes the main factor of the aero-thermo-radiation effect, which reduces the performance of these IR systems, or even makes these systems fail. By analyzing thermal radiation propagating in IR windows, a participating medium, an evaluation method for aero-thermo-radiation effect of the non-isothermal IR windows was proposed, based on the experimental results of the isothermal state, include self-radiation and transmittance. Aim to an MWIR detection system of a hypersonic vehicle, aero-thermo-radiation effect of a sapphire IR window was evaluated in 3.7-4.8 μm. The results indicate that, as the sapphire IR window is exposed in high-temperature and high-speed airflow, the aero-thermo-radiation effect of the window intensifies as temperature rises rapidly, the transmittance drops about 10%, still bigger than 0.9, otherwise the self-radiation enhances 458 times approximately, equal to that of blackbody about 125 ℃. For sapphire windows in 100-350 ℃, which thickness are smaller than 20 mm, as thickness increases, the transmittance decreases, self-radiation increases, and total radiation behind sapphire windows is increased, of which the ratio of self-radiation increases. So, self-radiation would drive detector into saturation easily, of which the influence on the MWIR detection system is bigger than that of transmittance.