Abstract: A set of preoperative CT reconstructed model can not be used in operating on individual patient in 3D surgical navigation systems. According to the problem above, a 3D bone morphing method based on Kriging algorithm was presented. Two point sets， one of which was acquired from physical space by the optical localizer and the other was from 3D model reconstructed by the marching cube method, were used to calculate the transformation matrix between the preoperative CT image space and the intraoperative marker space. Then 4 appropriate reference points were chosen to solve the equations based on Kriging algorithm, and the positions of points on CT model after deformation respect to the physical case were acquired. At last, precision analysis of morphing and evaluation experiment of knee joint navigation was carried out with CT and plastic model. The result shows that under this condition the final morphing accuracy is less than 1mm, and this technology can be used in operation evaluation of the anterior cruciate ligament navigation reconstruction.