In the structured light depth acquisition system, a system calibration method is proposed to reduce the measurement error when the heights of the projector system and camera system’s pupil centers are unequal.N frames orthogonal gratings and a cubic object are used to complete the calibration.Under the orthogonal light illumination, the shadow position of the cube and the grating line direction on the cube are served as references to complete the system coarse calibration.The phase modulated by the height of the cube in the horizontal direction is calculated to guide the system delicate calibration.This method can provide theoretical foundation for the system calibration and technical assistance for the researchers without experience in depth acquisition process.Experiment results demonstrate the effectiveness of the proposed method.