The present invention provides a human body security inspection method and system. The method comprises: retrieving in real-time scanning row or column image data of a personal to be inspected; transmitting in real-time the image data to an algorithm processing module and processing these image data by the module; automatically recognizing a suspicious matter by a suspicious matter automatic target recognition technique, after retrieving an image data of an entire scanning image of the personal; any of the following three inspection modes is selected, so as to perform a further processing on basis of the recognition result of the suspicious matter, (1) in a manner of automatic target recognition technique, (2) in a combination manner of the automatic target recognition technique and a privacy protection image; and (3) a combination manner of the automatic target recognition technique, a privacy protection image and human intervention.