Phase-based fringe projection metrology systems have been widely used to obtain the shape of 3D objects. One vital step is calibration, which defines the relationship between the phase and depth data. Existing calibration methods are complicated because of the dependence of the relationship on the pixel position. In this Letter, a simple calibration procedure is introduced based on an uneven fringe projection technique, in which the relationship between phase and depth becomes independent of the pixel position and can be represented by a single polynomial function for all pixels. Therefore, given a set of discrete points with a known phase and depth in the measuring volume, the coefficient set of the polynomial function can be determined. A white plate having discrete markers with known separation is used to calibrate the 3D imaging system. Experimental results demonstrate that the proposed calibration method is simple to apply and can build up an accurate relationship between phase and depth data.