The invention discloses an infrared vision based automatic landing guidance method and system applied to a fixed-wing UAV (unmanned aerial vehicle). The system comprises two identical image tracking modules, an image processing module, a control module and a wireless transmission module, wherein each image tracking module comprises a camera and biaxial pan-tilt units. According to the method, the UAV is detected, identified and tracked in images with an image tracking technology, and deflecting angles of the pan-tilt units are accurately recorded; the relative space position of the UAV can be determined through geometric relationship analysis and trigonometric calculation of pitch heading angles of the two pan-tilt units and the distance between the pan-tilt units, and position information of the UAV is sent to the UAV through the wireless transmission module, so that the UAV is guided to accurately land. The infrared vision based automatic landing guidance system is constructed on two sides of a landing runway of the UAV, complicated image processing is performed based on powerful computing capacity of a ground-based computer, each guidance device is utilized to the greatest extent, the accuracy of the system is improved, the control is simple, and real-time performance and stability are good.