The invention discloses a three-dimensional full face photographing system based on structured light projection and a photographing method thereof. The system comprises a processing unit and at least two measurement unit, wherein each measurement unit comprises a projection assembly, a photographing element and a synchronization module; the projection assembly projects a structured light video on the face of an acquired person, the photographing element photographs the face image of the acquired person and transmits the face image to the processing unit in a real-time mode, the synchronization module realizes synchronization between the photographing element and the projection assembly, and thus, the exposure time of the photographing element is included in out-light time when the projection assembly projects each frame of structured light video. Through arranging the measurement units at different positions, acquisition of the three-dimensional face image in a range of 180 DEG from a left ear to a right ear or from the right ear to the left ear can be realized, three-dimensional full face data are acquired through mosaic fusion, synchronization between each frame of structured light field image and the photographing element exposure time can be realized, the photographing time is shortened, and influences on the precision by movement of a human body during the photographing period can be reduced.