To evaluate the efficacy and safety of selective brain hypothermia (SBH) in the treatment of neonates with moderate or severe neonatal hypoxic-ischemic encephalopathy (HIE), and the effect of SBH treatment on serum levels of neuron-specific enolase (NSE) and central nervous specific protein S100. A prospective randomized controlled trial was conducted. From January 2015 to June 2017, 42 children with moderate to severe HIE in the neonatal intensive care unit (NICU) of the First Affiliated Hospital of Bengbu Medical College were enrolled, and they were randomly divided into SBH treatment group and routine treatment group after obtaining the consent of the guardian of the children. The children in routine treatment group were given the traditional symptomatic supportive treatment, supplemented by drugs to promote nerve cell growth. On the basis of traditional treatment, the children in the SBH treatment group were given SBH treatment within 6 hours after birth. The nasopharyngeal temperature was maintained at 33.0-34.5 centigrade and the rectal temperature was maintained at 34.5-35.0 centigrade. The general clinical data of the two groups including gender, gestational age, birth weight, age, 5-minute neonatal asphyxia score (Apgar score), score for neonatal acute physiology perinatal extension version II (SNAPPE II) were collected. The primary outcomes were hospitalized death, severe disability at 15 months of age, neonatal behavioral neurological assessment (NBNA) score at 28 days of age, and Bayley scales of infant development (BSID) score [including mental development index (MDI) score and psychomotor development index (PDI) score] at 15 months of age at follow-up. The secondary outcomes were serum levels of NSE and S100 protein. The occurrences of adverse events in the two groups were recorded. Among 42 HIE children, 1 child of severe congenital malformation and 1 child of platelet count (PLT) < 50×109/L were excluded, and 40 children were enrolled in the study group. During the follow-up period, 2 children of SBH treatment group and 2 children of routine treatment group were lost or the outcome was unknown. Finally, 18 children of each group were enrolled in the analysis. There was no significant difference in the baseline data of gender, gestational age, birth weight, age, 5-minure Apgar score or SNAPPE II score between the two groups, indicating that the baseline data of the two groups were balanced and comparable. The incidence of severe disability in the SBH treatment group was significantly lower than that in the routine treatment group [5.6% (1/18) vs. 44.4% (8/18), P < 0.05]. There was 1 child death in the routine treatment group and no death in the SBH treatment group. Compared with the routine treatment group, the 28-day NBNA score of the SBH treatment group was increased by 2.9 [95% confidence interval (95%CI) = 1.0-4.8], BSID score at 15 months of age was improved significantly, MDI score was increased by 11.8 (95%CI = 4.3-19.3), and PDI score was increased by 12.4 (95%CI = 2.5-22.3), with significant differences between the two groups (all P < 0.05). After 3 days of treatment, the serum NSE and S100 protein levels in both groups were significantly decreased as compared with those before treatment [NSE (μg/L): 30.15±15.18 vs. 31.32±14.75, S100 (ng/L): 387.5 (273.3, 573.0) vs. 890.0 (590.5, 1 162.5) in routine treatment group; NSE (μg/L): 29.09±16.22 vs. 32.25±15.43, S100 (ng/L): 402.5 (302.2, 580.5) vs. 842.0 (462.3, 1 200.5) in SBH treatment group, all P < 0.05]. There was no significant difference in serum NSE or S100 protein level between the two groups (all P > 0.05). There was no serious adverse event such as arrhythmia, large vein thrombosis or irreducible hypotension in both groups, and there was no significant difference in the incidence of general adverse events such as sinus bradycardia, scleredema, blood glucose disorder, or systemic infection between the two groups [16.7% (3/18) vs. 11.1% (2/18), 5.6% (1/18) vs. 5.6% (1/18), 22.2% (4/18) vs. 11.1% (2/18), 5.6% (1/18) vs. 5.6% (1/18), all P > 0.05]. SBH treatment could significantly increase the NBNA score at 28 days of birth and BSID score at 15 months of age, reduce the incidence of severe disability in moderate and severe HIE children, but it was not be proved that SBH could reduce the mortality. Compared with routine treatment, SBH treatment had no significant superiority on improving the levels of serum NSE and S100 protein, suggesting that SBH could not protect the brain by inhibiting the apoptosis of nerve cells and promoting the repair of nerve cells.