In order to study the anti-disturbance characteristic of the Micro Air Vehicle (MAV) with flexible aerodynamic shape, a hovering MAV with flexible aerodynamic shape was designed, and the finite element method was used to conduct modal analysis of its vertical airway. Then, its vertical lift and hovering were achieved. The preliminary three-dimensional visual inspection of the aircraft was completed in an airflow disturbance experimental device, which is based on binocular stereo vision. The aircraft’s motion trace and morphological changes of the aerodynamic shape under airflow disturbance were recorded using stroboscopic imaging technique, which provided an effective extraction method for studying the unsteady aerodynamic characteristic of the flexible aerodynamic shape and the anti-disturbance mechanism of hovering MAV.