When hypersonic vehicles have high-hypersonic flights in the atmosphere, high-temperature IR windows become the main factor of complicated aero-thermo-radiation effects, which would reduce the performance of IR detection systems, or even make these systems fail. By analyzing thermal radiation transfer in IR windows, an experimental platform is established to measure thermo-radiation characteristics of IR window materials. And a method is proposed to evaluate thermo-radiation characteristics of IR windows with uneven temperature distribution. Take a MWIR detection system of a hypersonic vehicle as an example, thermo-radiation characteristics of a sapphire IR window is evaluated. The results indicate that, thermo-radiation characteristics of the sapphire IR window material in 3.7μm-4.8μm have an approximate cubic relationship with temperature at 100°C~350°C. With the rise of temperature, the transmittance of the sapphire material decrease, while the window self-radiation increase. As the sapphire IR window is exposed in high-temperature and high-speed airflow, the transmittance drops 4%, still bigger than 95%, self-radiation enhance about 9 times, while temperature of the window rises rapidly. Self-radiation can drive detector into saturation easily, of which the influence on the MWIR detection system is bigger than that of transmittance.