Objective To compare the value of CT and MRI diagnosis of neonatal hypoxic-ischemic encephalopathy (HIE). Methods Based on clinical and radiographic universal indexing standards, a retrospective analysis of 60 cases of HIE clinical and CT, MRI data was analyzed, The clinical and imaging division compliance rate using the chisquare test, with P<0.05 level for statistical learn the difference was significant. Results 60 cases were all underwent CT, while 25 patients underwent MRI. Clinical grading: 29 mild cases (48.3%) , 21 moderate cases (35%), 10 severe cases (16.7%); CT indexing: normal in 7 cases (11.7%), mild in 24 cases (40%), moderate in 20 cases (33.3%), and severe in 9 cases (15%), 21 cases of intracranial hemorrhage (35%). HIE detection rate of 88.3%. According to clinical grading standard, CT diagnostic agreement was 82.4%, X2 =10, P=0.019 <0.05. MRI examination of 25 cases: mild in 12 cases (48%), moderate in 9 cases (36%), severe in 4 cases (16%), intracranial hemorrhage in 6 cases (24%). HIE detection rate of 100%, consistent with the clinical grading by 93.5%. CT scan of mild to moderate HIE display rates were 6.5%, 45%, MRI were 25.3%, 58.3%. Conclusion CT and MRI have significant value in the early diagnosis, classification and prognosis of HIE, MRI is superior to CT; But CT detection of subarachnoid hemorrhage is superior than MRI.