Generally, simplified calibration models are preferred in existing reconstruction algorithms for fringe projection profilometry (FPP) to improve numerical stability. However, the lens distortions of the camera and the projector of a FPP system cannot be compensated effectively with such a simplified calibration model and the measurement accuracy of FPP cannot be assured as a result. Therefore, a two-step calibration method, in which lens distortion compensation and system calibration are performed successively, is presented. The lens distortion compensation is performed by correcting the values of input variables with calibrated parameters of the camera and the projector. Therefore, lens distortions of the camera and the projector can be compensated effectively, and 3D shape data with higher accuracy can be retrieved accurately with a concise calibration model. The validity and practicality of the proposed method are verified with experimental results.