Remarkable progress has been made in satellite-based quantum key distribution (QKD), which can effectively provide QKD service even at the intercontinental scale and construct an ultralong-distance global quantum network. But there are still some places where terrestrial fiber and ground stations cannot be constructed, like harsh mountainous areas and air space above the sea. So the airborne platform is expected to replace the ground station and provide flexible and relay links for the large-scale integrated communication network. However, the photon transmission rate would be randomly reduced, owing to the randomly distributed boundary layer that surrounds the surface of the aircraft when the flight speed is larger than 0.3 Ma. Previous research of airborne QKD with boundary layer effects is mainly under the air-to-ground scenario in which the aircraft is a transmitter, while the satellite-to-aircraft scenario is rarely reported. In this article, we propose a performance evaluation scheme of satellite-to-aircraft QKD with boundary layer effects in which the aircraft is the receiver. With common experimental settings, the boundary layer would introduce a ∼31dB loss to the transmitted photons, decrease ∼47% of the quantum communication time, and decrease ∼51% of the secure key rate, which shows that the aero-optical effects caused by the boundary layer cannot be ignored. Our study can be performed in future airborne quantum communication designs.