Objective To investigate the diagnosis value and comparative analysis of CT and MRI in the diagnosis of viral encephalitis. Methods Retrospectively analyze clinical and CT + MRI data of 41 patients confirmed through cerebrospinal fluid routine examination in our hospital from April 2013 to May 2016, and compare image difference and diagnostic accuracy of the two inspection methods on viral encephalitis. Results Among 41 patients, 32 cases are identified as viral encephalitis through CT imaging, while 4 cases are misdiagnosed as other diseases, and 5 cases are missed due to no abnormal image display. The positive detection rate was 78.0%. While after MRI inspection, 38 patients are correctly diagnosed as viral encephalitis among 41 patients, 1 case is misdiagnosed and 2 cases are missed. The positive detection rate was 92.7%. Conclusion CT and MRI both have typical imaging characteristics of judgment in the diagnosis of viral encephalitis, which can provide the lesion location, shape and other characteristics parameters. However, MRI scanning in diagnosis of viral encephalitis turns out be more accurate and of lower misdiagnosis rate, whose diagnosis rate is significantly higher than CT scanning. Therefore, the application value of MRI higher and it is worthy of further promotion.