To reduce the speckle phenomenon caused by atmospheric boundary layer on an optical window in airborne laser communication, the aero-optics effect and corresponding suppression method for the atmospheric boundary layer were discussed. Based on the type of experimental airplane and the position of equipment installation, the parameters of shape, thickness of the optical window were designed optimally, and the deformation of optical window and air flow field distribution were analyzed in the simulation and the optical window was improved. Finally, a series of compensating glasses were developed to solve defocusing of the receiving spot caused by the atmospheric boundary layer. A flight experiment was performed at the flight distance of 10-140 km and the flight altitude of 1 500-4 500 m and the compensation results were analyzed. The results show when the compensating glass with final focal length of 5.5×105 m is added into the receiving optical path, the atmospheric boundary layer is actively restrained by compensated optical window, the shape of receiving spot is improved and the receiving power distribution variance is reduced by 1/3. These results mean that the window after compensation reduces the effect of atmospheric boundary layer on laser communication effectively.