Objective: To investigate the diagnostic value of integrated brain and neck vascular ultrasound in differentiating occlusion of the intracranial segment of the vertebral artery (VA) from vertebral artery hypoplasia, and to analyze the differences in hemodynamic characteristics between the two conditions. Methods: A total of 54 patients with intracranial vertebral artery occlusion (occlusion group) and 48 patients with vertebral artery hypoplasia (hypoplasia group), all of whom underwent integrated carotid ultrasound and transcranial doppler (TCD) examination, were included. Carotid intima-media thickness (IMT) and plaque characteristics were measured. Peak systolic velocity (PSV), end-diastolic velocity (EDV), pulsatility index (PI), and resistance index (RI) were recorded at the intervertebral and intracranial segments of the vertebral artery, the middle cerebral artery, and the basilar artery, along with collateral circulation status. Binary Logistic regression analysis was used to identify independent differentiating factors, and receiver operating characteristic (ROC) curves were employed to evaluate the diagnostic performance of each parameter. Results: In the occlusion group, IMT, plaque detection rate, and the proportion of unstable plaques were all higher than those in the hypoplasia group (P<0.05). On the affected side, PSV and EDV of the vertebral artery at the intervertebral segment decreased, while RI increased. In the intracranial segment, PSV, EDV, and RI on the affected side were all lower, whereas PSV and EDV on the contralateral side were higher. PSV, EDV, and PI of the middle cerebral artery and basilar artery decreased, and the patency rate of the posterior communicating artery increased (P<0.05). Decreased intracranial PSV on the affected side, increased IMT, increased ΔRI on the affected side, and a patent posterior communicating artery were independent predictors of occlusion (P<0.05). The combined model achieved an AUC of 0.958 (95%CI:0.923~0.993), with a sensitivity of 92.59% and a specificity of 89.58%, outperforming any single parameter (P <0.05). Conclusion: Intracranial VA occlusion and VA hypoplasia exhibit distinct hemodynamic profiles. Integrated brain and neck vascular ultrasound enables systematic evaluation of hemodynamic alterations throughout the extracranial and intracranial course of the VA, as well as other cervicocerebral vessels, demonstrating substantial clinical utility in the differential diagnosis of these two entities.