With the growing importance of esthetic considerations, soft-tissue evaluation plays a crucial role in maxillofacial treatment, including the establishment of normative anthropometric database, treatment planning, and postoperative evaluation. In therapy, three-dimensional (3D) photography techniques with high reproducibility, such as cone beam computed tomography (CBCT), 3D stereo-photography, and laser scanning technology, can facilitate the comprehensive oral and maxillofacial assessment different from direct and 2D measurements. 3D photography is faster, more precise, more automatic and less harmful than the traditional methods. A universal standard for 3D-maxillofacial morphology has not been established, thus limiting the clinical applications of 3D stereo-photography. Natural head position is the most direct reference to maxillofacial assessment. However, the lack of a standardized method of correcting natural head position is the main factor that limits the use of 3D stereo-photography. Therefore, a versatile method for correcting accurate and reliable head position is needed. In this paper, several methods for recording and correcting the natural head position based on 3D stereo-photography were discussed. The difference between the correction procedure based on 3D stereo-photography and CBCT were compared, and the optimal approach for correcting natural head position in 3D scale was determined.