An important step of phase calculation-based fringe projection systems is 3D calibration, which builds up the relationship between an absolute phase map and 3D shape data. The existing 3D calibration methods are complicated and hard to implement in practical environments due to the requirement of a precise translating stage or gauge block. This paper presents a 3D calibration method which uses a white plate with discrete markers on the surface. Placing the plate at several random positions can determine the relationship of absolute phase and depth, as well as pixel position and X, Y coordinates. Experimental results and performance evaluations show that the proposed calibration method can easily build up the relationship between absolute phase map and 3D shape data in a simple, flexible and automatic way.