An auto focus photographing system applied in an electronic device that is worn before eyes of a user is provided. The auto focus photographing system includes a first camera module, a second camera module, and a processor. The first camera module captures images of the eyes. The second camera module captures images of objects that the eyes focus on. The processor analyzes a distance between centers of eye pupils of the user and calculates a focusing current value corresponding to the distance, and adjusts a focus distance of the second camera module accordingly. The processor detects a capture command and the second camera module captures an image according to the adjusted focus distance. An electronic device employing the auto focus photographing system is also provided.