The human spatial orientation system is well designed on the ground but is imperfect in the aeronautical three-dimensional (3D) environment. However, human perception systems perform Bayesian statistics based on encountered environments and form shortcuts to improve perceptual efficiency. It is unknown whether our perception of spatial orientation is modified by flying experience and forms perceptual biases. The current study tested pilot perceptual biases on ambiguous visual stimuli, the bistable point-light walkers, and found that flying experiences increased the pilot's tendency to perceive himself as higher than the target and the target as farther away from them. Such perceptual effects due to flight are likely to be attributed to experience of variable vestibular state in a higher position in 3D space, rather than the experience of a higher viewpoint. Our findings suggest that flying experience will modifies our visual perceptual biases, and that more attention should be paid to the enhanced viewing from above bias when flying to avoid overestimating altitude or viewing angle when the visual conditions are ambiguous.