With the substantial progress of terrestrial fiber-based quantum networks and satellite-based quantum nodes, airborne quantum key distribution (QKD) is now becoming a flexible bond between terrestrial fiber and satellite, which is an efficient solution to establish a mobile, on-demand, and real-time coverage quantum network. However, the random distributed boundary layer is always surrounded to the surface of the aircraft when the flight speed larger than 0.3 Ma, which would introduce random wavefront aberration, jitter and extra intensity attenuation to the transmitted photons. In this article, we propose a performance evaluation scheme of airborne QKD with boundary layer effects. The analyzed results about the photon deflection angle and wavefront aberration effects, show that the aero-optical effects caused by the boundary layer can not be ignored, which would heavily decrease the final secure key rate. In our proposed airborne QKD scenario, the boundary layer would introduce ∼3.5 dB loss to the transmitted photons and decrease ∼70.7 % of the secure key rate. With tolerated quantum bit error rate set to 10 %, the suggested quantum communication azimuth angle between the aircraft and the ground station is within 60 • . Furthermore, the optimal beacon laser module and adaptive optics module are suggested to be employed, to improve the performance of airborne QKD system. Our detailed airborne QKD performance evaluation study can be performed to the future airborne quantum communication designs.