The invention discloses a bionic-based flying mechanical neck eye system and a control method thereof. The system involves an aircraft system, a mechanical neck eye system, an airborne computing device and a flight control unit; the mechanical neck eye system involves a mechanical neck arranged on an aircraft body, a binocular vision inertia system arranged at the tail end of the mechanical neck,and a mechanical neck main control for controlling the movement of the mechanical neck; and the binocular vision inertial system involves a binocular camera and an inertial measurement unit, the binocular vision inertia system is used for carrying out active observation and completing pose estimation on the tail end of the mechanical neck, and the mechanical neck is a six-degree-of-freedom seriesmechanical neck. According to the bionic-based flying mechanical neck eye system and the control method thereof, the binocular vision inertial system consisting of the double fisheye cameras and the inertial measurement unit is placed at the tail end of the mechanical neck to form a sensing system, so that the observation range of the system is larger; and the cameras is variable in pose, and hasthe capability of actively sensing the environment, so that the problem that the view field of an aircraft in the indoor environment is limited can be solved to a certain extent, and meanwhile, the shaking of pictures can be compensated.