Objective To explore the accuracy of double modality fusion between CT and MRI for human head, based on pair anatomical points registration. Methods CT and MRI were approached in 4 patients, digital imaging and communications in medicine (DICOM) files were loaded on 3D Slicer (version 4. 8.1), the surface and brain were reconstructed automatically with volume rendering as reconstructed models, 10 surface characters were tested with localization error and would be used as fiducial points, 8 of the points would be chosen as pairpoints for registration according the localizing error after 5 localizations, 5 registration groups based on 4, 5, 6, 7, 8 fiducial points were divided. Singular value decomposition (SVD) was employed for registration as a basic algorithm, and fiducial registration error (FRE) was used to evaluate the registration error. Results FRE values of double modality fusion were 2.68-6.54 mm. FRE values of 4, 5, 6, 7, 8 fiducial points were (5.14±0.97)mm, (4.71±0.64)mm, (4.45±0.59)mm, (4.13±0.55)mm, (3.54±0.72)mm respectively. There was no statistical difference between neighbor groups, while in 4 and 8 points groups, the FRE values were different statistically. Conclusion Surface anatomic characters can be used for double modality fusion between CT and MRI; FRE values after CT-MRI double modality fusion are reduced with the increase of points.