This study aimed to quantitatively evaluate thrombus length and its relationship with the severity and prognosis of acute cerebral infarction using high resolution CUBE imaging. National institute of health stroke scale (NIHSS) score and modified rankin scale (mRS) score were used to quantify the degree of neurological impairment and the prognosis of patients. The length of cerebral artery thrombosis was measured with CUBE imaging. Strong relationship was revealed between the thrombus length and NIHSS or mRS score. We therefore demonstrated that thrombus length measurement based on CUBE MRI can effectively evaluate the severity and prognosis of acute cerebral infarction.