Objective To investigate the value of CT and MRI in detecting neonatal hypoglycemic brain injury. Methods of the imaging data of 35 neonatal hypoglycemia patients who underwent CT and MR examinations in our hospital from January 2015 to January 2017 were analyzed retrospectively. Then the typical imaging features of CT and MRI were compared and the influenced factors were analyzed. Results The MRI detecting rate of abnormal neonatal hypoglycemic brain injury was significantly higher than of CT (P<0.05), the good rate of MRI diagnosis was significantly higher than that of CT (P<0.05). While the detecting rate of moderate and severe neonatal hypoglycemic brain injury was significantly lower than of CT (P<0.05), no difference was found in the death diagnosis rate (P>0.05), the typical imaging features of CT including patchy clouding opacity, secondary hydrocephalus, iso density in the cerebral lateral chamber. The typical imaging features of MRI including low signal on T1 weighted image and high signal on T2 weighted image after the 2 days of hemorrhage; high signal on T1 weighted image and low signal on T2 weighted image within 12 days of hemorrhage; low signal on T1 weighted image and high signal on T2 weighted image after 13 days of hemorrhage. Mode of delivery and gestational hypertension were not correlated with neonatal hypoglycemic brain injury (P>0.05). Diabetes mellitus, premature infant / low birth weight infant children, first lactation time > 24h, blood glucose <2.2mmol/L and duration of hypoglycemia > 24h were the independent risk factors of neonatal hypoglycemic brain injury (P<0.05). Conclusion Compared with CT examination, MRI has a higher diagnostic rate of neonatal hypoglycemic brain injury, which can improve the detection rate of neonatal hypoglycemic brain injury.