Precision registration of serial sections is an important step for 3-D image reconstruction. It directly affects the accuracy of the reconstructed result and parameter computation. This problem has been studied and demonstrated by many investigators, but the whole process has not yet reached good performance. In this paper, we discussed the registration of serial sections image of mandible and put forward a method of the soft registration-based transformation on the basis of the hard registration in consideration of the speciality of 3-D image reconstruction for the serial sections of mandible. Employing control points and using Affine Transformation and Extended Hough Transformation, we solved the problem of displacement on 3-D image reconstruction for serial secons and paved the way for reconstructing the mandible microstructure with reality. The results of experiments indicate that the 3D image reconstructed after registration has only a little distortion.