One important step of phase-based three-dimensional imaging system is calibration, which defines the relationship between phase and depth data. Existing calibration methods are complicated and hard to carry out because of using a translation stage or gauge block in a laboratory environment. This Letter introduces a new simple, flexible calibration method by using a checkerboard and a white plate having discrete markers with known separation. The checkerboard determines the internal parameters of a CCD camera. The plate gives phase and depth data of each pixel to establish their relationship. Experimental results and performance evaluation show that the proposed calibration method can reliably build up the accurate relationship between phase map and depth data in a simple, flexible way.