Objective: To explore the clinical related factors of neonatal hand-foot-mouth disease (HFMD) complicated with encephalitis.Method: The neonatal HFMD complicated with encephalitis treated in our hospital from July 2015 to July 2020 was taken as the object of study. According to the NBNA score at discharge, the patients were divided into normal group and abnormal group. The clinical symptoms, auxiliary examination and prognosis of the two groups were compared.Result: (1) General condition: there was no significant difference in sex, age, duration of fever, treatment time and etiological test between the two groups (P > 0.05). (2) Clinical symptoms and signs: there was significant difference in abnormal consciousness between the two groups (P < 0.05). However, there was no significant difference in skin rash, respiratory system symptoms, digestive system symptoms, signs of high intracranial pressure, increased muscle tone and weakening of primitive reflex (P > 0.05). (3) Auxiliary examination: the number of white blood cells and the level of cytokines (CK-BB, UCH-L1) in cerebrospinal fluid (CSF) in the group with abnormal NBNA score were significantly higher than those in the group with normal NBNA score (P < 0.05). The serum IgM level in the abnormal NBNA score group was higher than that in the normal NBNA score group, and the serum IgG level in the abnormal NBNA score group was lower than that in the normal NBNA score group, and the difference was statistically significant (P < 0.05). The abnormal rate of Craniocerebral MRI in abnormal NBNA score group was higher than that in normal NBNA score group, and there was significant difference between the two groups (P < 0.05). There was no significant difference in the levels of protein, sugar, chloride, lactate dehydrogenase, and MMP-9 in CSF and the abnormal rate of amplitude integrated EEG (aEEG) between the two groups (P > 0.05). (4) The prognoses of patients with normal and abnormal NBNA score are good, and there are not significantly differences in the prognosis between the two groups (P > 0.05).Conclusion: (1) Neonatal HFMD complicated with encephalitis occurs more than 10 days after birth, there is no obvious abnormality in male and female, the vast majority of newborns have febrile symptoms, rash is not its specific manifestation, and most of them are atypical. (2) The positive rate of HFMD-related virus detected in CSF of neonatal HFMD is high. For newborns with abnormal consciousness, CSF examination should be accomplished in time, which has certain clinical significance for early diagnosis and treatment of severe newborns. (3) The increase of white blood cell count and cytokines (CK-BB, UCH-L1) in CSF of neonatal HFMD complicated with encephalitis has a certain clinical reference value for early diagnosis and identification of severe newborns. (4) There is a certain humoral immune disorder in newborns with HFMD complicated with encephalitis, but the overall prognosis is better due to the protective effect of maternal IgG.