Objective This paper is to investigate and compare clinical value of CT and MRI in early diagnosis of acute cerebral infarction and to provide the reference for clinical treatment. Methods Sixty five patients admitted by the Department of Internal Medicine in the manner of controlled study were compared, all patients were subject to craniocerebral CT and MRI examination in 6 hours after attacks of diseases to determine conditions of disease, and advantages and disadvantages of two diagnostic modewere compared. Results The diagnosis rate of CT examination was 69.23%,and that of combined MRI on the basis of CT was 96.92%, thedifference was significant when two methods were compared (P<0.05). The detected lesion locations of two examination modes were the lobe, basal ganglia and cerebellum, MRI could detect brainstem infarction, but CT failed to detected it. The comparison in the diameter of detected lesion via two examination method satisfied P＜0.05, and the difference was significant. Conclusion MRI diagnosis applied in early acute cerebral infarction can clearly display the position, shape and size, being conductive to clinically early diagnosis on disease. Combined CT diagnosis is of high diagnosis accuracy and wide prospect of clinical applications