Objective To evaluate the techniques of separating, fusing, opacifying and falsecoloring- volume rendering( SFOF-VR)3D imaging on the bone and blood vessels in the region of atlantoaxial joint(AAJ). Methods SFOF-VR 3D imaging was performed on 35 cases, including normal (n = 6),variations and lesions( n =29), which were selected from cases with the head-neck CTA examination. With the original scanning data, the VR imaging was performed, then SFOF-VR imaging. Comparisons were made between the features of 3D images of SFOF-VR and VR in showing the anatomy, diagnosing the variation and lesion of AAJ and VA, and the results were analyzed by using the Fisher exact test. Results The results of 35 cases included 6 normal cases in the region of atlantoaxial joint and VA, 16 variations in atlantoaxial joint or VA, 6 cases with arteriosclerosis in VA and 7 cases with fracture or dislocation of atlantoaxial joint. All SFOF-VR imaging are satisfactory. SFOF-VR imaging can show the atlas, epistropheus and VA independently or jointly, cut or color the structures freely and get 3D measurements in any direction.Comparisons showed that SFOF-VR images were much clearer and more comprehensive than VR in displaying the anatomy, variation and lesions of AAJ and VA. Statistical differences were found in showing the spatial structure, blocking structure, space measurement, variation and disease and image edge ( there are25,7,3,0, 31,3,1,0, 26,3,6,0, 23,7,5,0, 0,10,20,5 cases for SFOF-VR image with excellent,good, ordinary and poor quality, and 2,5,24,4, 0,2,8,25, 0,7,25,3, 5,6,23,1, 29,4,2,0 cases for VR;χ2 values 40. 259, 61.444, 42.245, 24.220, 51.299, P<0. 01 ). Conclusions SFOF-VR is a new 3D imaging technique which can clearly and directly show the bones and blood vessels in the region of AAJ.It can provide anatomical information for imaging diagnosis and surgical operation.