Morphological features of vascular have a major impact on blood flow and chronic diseases. A 3D semi-automatic vessel geometric feature extraction algorithm was developed in this study, and applied to basilar artery (BA). The relationship among BA morphological parameters can be explained by hemodynamic and flow mechanism. The geometry of BA affected the cerebral blood flow value was demonstrated in this study. This algorithm will save us a lot of efforts for analyzing large dataset, and help clinical doctors to quantify the vessel morphometry rapidly.