Objective To investigate the clinical application value of EEG on hand foot mouth disease combined with encephalitis. Methods from January 2011 to December 2015, a total of 60 cases of HFMD in our hospital from mouth disease combined with encephalitis were selected as observation group, select the same period from HFMD patients without encephalitis in 60 cases as control group in all, EEG of all patients, the EEG detection results of the two groups were compared. Results The observed EEG of 60 cases were abnormal, the abnormal rate was 100%, the control group of 60 cases in the detection of EEG abnormalities in 8 cases, the abnormal rate was 13.3%, compared with the control group, the abnormal rate of observation group was significantly higher EEG detection, P<0.05. observation group with EEG of 14 mild cases, 28 moderate cases and 18 severe cases, more serious clinical symptoms, EEG abnormalities were more serious. Conclusion EEG can assist Assistant foot mouth disease combined with encephalitis in children with early clinical diagnosis, and can assist in the diagnosis of children with disease severity, clinical use of EEG detection of children with disease status, assisted hand foot mouth disease combined with encephalitis treatment effect detection.