Objective: This study aims to investigate the correlation between cerebral blood flow (CBF) values and neonatal behavioral neurological assessment (NBNA) in hypoxic-ischemic encephalopathy (HIE), the relationship between early CBF value changes and the prognosis of neonatal HIE, and the consistency between the clinical grading and magnetic resonance (MR) grading of HIE. Methods: Forty neonates with HIE were scanned using the three-dimensional arterial spin labeling (ASL) sequencing of the cranial Magnetic Resonance Imaging (MRI). These newborns were classified as having mild, moderate and severe HIE, according to the clinical grading, and as being normal or having mild, moderate, or severe HIE, according to the MRI grading. Then, the consistency of these two grading systems was compared. Afterwards, the differences in the CBF values of neonates in groups with mild, moderate and severe HIE were compared. In addition, these neonates were grouped according to their NBNA scores. A score of >= 35 was considered a good prognosis, while a score of <= 35 was considered a poor prognosis. The differences in CBF values between these two groups were compared, and the correlation between the CBF values and NBNA scores was determined. Results: There was a strong consistency between the evaluation results for the clinical grading and MR grading (kappa value = 0.672, P<0.001). The differences in CBF values for the basal ganglia (BG) area and thalamus, and the differences in NBNA scores for groups with mild, moderate, or severe HIE were statistically significant (P<0.05). The differences between the poor prognosis group and the good prognosis group, in terms of the CBF values for the BG area and thalamus, and the NBNA scores were statistically significant (P<0.05). The CBF values in the BG region and thalamus were closely and negatively correlated with the NBNA scores. Conclusion: Early CBF values in the BG area and thalamus can objectively and visually reflect the severity of the HIE, and be used to predict the outcome of functional brain damage, allowing early neuroprotective treatment to be initiated. The higher the perfusion in the BG region and thalamus, the lower the NBNA score, and the worse the prognosis would likely be. ASL combined with the NBNA score provides a more comprehensive classification for HIE and a more accurate assessment of the clinical prognosis, providing more medical imaging information for early clinical treatment.