Phase calculation-based fringe projection techniques have been an excitement for three-dimensional (3D) shape measurement. The accuracy of a measurement system is mainly hindered by the calibration accuracy. Existing calibration methods are subjected to the low accuracy because planar boards with checker, ring or dots are used to provide only limited number (tens to hundreds) of reference points with lower accuracy (pixel level). In this paper, a novel 3D calibration method is proposed by using a liquid crystal display (LCD) screen to offer high density reference points. A refraction model of the LCD screen is established to reduce phase error introduced by the refractive index and the coating thickness of the screen. Placing the LCD screen at several positions parallel to each other in front of the camera can determine not only the relationship of absolute phase and depth, but pixel position and X, Y coordinates. Experimental results demonstrate that the proposed 3D calibration method achieves the higher measurement accuracy of the shape data compared with the existing state of the art methods.