The objective of this article is to display the vertebral artery and bone structure at the craniocervical junction (CJVA and C(0-1-2)) with three-dimensional CT angiography (3DCTA) and identify their anatomic features and variations. Eighty-eight subjects without pathology of vertebral artery (VA) and C(0-1-2) were selected from head-neck CTA examination. 3D images were formed with volume rendering (VR) and multiplanar reconstruction (MPR). On the 3D images, CJVA and C(0-1-2) were measured, and their variations were observed. CJVA goes along C(0-1-2) with five curves, of which three curves are visibly away from C(0-1-2), one is 0.0-8.3 mm away at the second curve with 0.0-11.2 mm in width, another is 0.0-9.2 mm away at the fourth with 2.8-14.8 mm and the other is 0.0-6.2 mm away at the fifth. Statistical comparisons show that there is no significant difference in the measurements between left and right, and that the curves become smaller and farther away from C(0-1-2) with the increase of age. CJVA is not equal in size, with the biggest in the fourth curve and the smallest in the fifth. Statistical comparison shows the left CJVA is larger than the right in the fifth curve. Variations were found on CJVA in 16 cases and on C(1) in 12 cases. The anatomy and variations of CJVA and C(0-1-2) are complicated. It is of vital significance to identify their anatomic features in clinical practice.