This paper transfered the problem of the 3D craniofacial registration into the one in 2D parameter domain by using surface parameterization. Firstly, six landmarks on the craniofacial surfaces were calibrated according to the physiological characteristics, and the pose and size of the craniofacial surfaces were normalized by projecting the craniofacial surfaces into a unified coordinate system which was determined by using the six landmarks. Secondly, Least Squares Conformal Mapping (LSCM) was performed for a reference craniofacial surface by pinning two outer corners of the eyes, by which the 2D parameters of the six landmarks were computed. Thirdly, any craniofacial surface could be mapped into a 2D domain using LSCM by pinning the six landmarks. Finally, the 3D point correspondences were obtained by mapping the 2D correspondences into the 3D surfaces. To validate the proposed method, the reference model was deformed into the target one by the Thin Plate Spline (TPS) transform with the corresponding vertices being control points, and the average distance between two corresponding point sets after deformation was computed. By the average distance, the proposed method was compared with the principal axes analysis based ICP (Iterative Closest Point) and the random sampling control points based iterative TPS registration methods. The comparison shows that the proposed approach is more accurate and effective.