The invention discloses an in vivo detection method and a system based on the physiological motion of face, pertaining to the face recognition field. The method includes that: Step A. detecting a motion region and a motion direction of the object within the imaging view of the detection system, and locking a face detection result frame; Step B. judging whether a valid face motion exists in the face detection result frame, if not, a picture face is determined, and if it is, turn to the Step C; Step C. judging whether the face motion in the face detection result frame is a physiological motion, if not, a picture face is determined, and if it is, an actual face is determined. The system comprises a motion detection module, a valid-face-motion judgment module and a physiological motion judgment module. The technical proposal in the invention can discriminate actual face and picture face, and enhance the reliability of the face recognition system.