To observe the change of heart rate variability (HRV) in newborns with hyperbilirubinemia, and to discuss the influence of hyperbilirubinemia on autonomic nerve function in newborns. Methods: We selected for this study 162 newborn infants treated in our hospital for hyperbilirubinemia. According to whether indexes of exchange transfusion was achieved and whether exchange transfusion therapy was received, patients were divided into Group A (neither achieved indexes of nor received transfusion, n=89), Group B (achieved indexes of but did not receive transfusion, n=34), and Group C (achieved indexes of and received transfusion, n=39). An additional 50 healthy newborns were selected as the control group. Indexes of HRV of the three patient groups before and after treatment were analytically compared with that of the control group. Results: Before treatment, there was no significant difference between Group A and the control group in all indexes of HRV (all P>0.05). Compared with the control group, standard deviation of R-R intervals (SDNN), total power (TP), and high frequency (HF) of Groups B and C before treatment were decreased (all P<0.05). After treatment, there was no significant difference between Group A and the control group in all indexes of HRV (all P>0.05). SDNN and HF of Group B and SDNN, TP, and HF of Group C were increased after treatment (all P<0.05), and SDNN of Group C was higher than that of Group B (P<0.05). Spearman linear correlation analysis showed that SDNN and HF were negatively correlated with level of total serum bilirubin (r=－0.217, －0.266; P= 0.000). Conclusion: HRV is a reliable indicator of the severity of neonatal hyperbilirubinemia. For newborns with severe hyperbilirubinemia, exchange transfusion was effective in improving autonomic nerve function.