Abstract: Objective To analyze the dynamic expressions and prognostic values of serum neuron-specific enolase (NSE) and copeptin in neonates with hypoxic-ischemic encephalopathy (HIE). Methods A total of 86 children with HIE treated in Tongchuan Maternal and Child Health Hospital from February 2014 to December 2015 were selected as the case group, 42 healthy neonates born during the same period were assigned to the control group. The serum levels of NSE and copeptin in the subjects were measured at 12, 24, 72, and 168 h after birth. The relationship between the levels of NSE and copeptin and the scores of neonatal neurobehavioral assessment (NBNA) and intellectual development scale (CDCC) were analyzed at different time points. The effect of NSE and copeptin at different time points on prognosis was also evaluated. Results According to the follow-up results, 25 cases of HIE patients had a poor prognosis, and 61 cases had a good prognosis. The levels of serum NSE and copeptine were higher in the case group at different time points than those in the control group (P<0.05). NBNA score and CDCC score in the case group were lower than those in the control group (P<0.05). The levels of serum NSE and copeptin at different time points were higher in the severe children than those in the mild and moderate children (P<0.05), and the levels of serum NSE and copeptin at different time points were higher in the moderate children than those in the mild children (P<0.05). The levels of serum NSE and copeptin at different time point in the poor prognosis group were higher than those in the good prognosis group (P<0.05). Serum NSE and copeptin levels at different time points were negatively correlated with NBNA score and CDCC score of HIE children, and the area under ROC curve (AUC) of NSE and copeptin alone or jointly predicted poor prognosis was greater than 0.6. Conclusions The serum levels of NSE and copeptin in children with HIE increase significantly, which is related to the severity and prognosis of the disease. Early joint detection of serum NSE and copeptin levels can increase the accuracy of predicting poor prognosis.