Hyperbilirubinemia is a common disorder in neonates, with premature infants at higher risk of developing the disorder. Glucose-6-phosphate dehydrogenase (G6PD) gene detection was used to determine the incidence of G6PD deficiency and analyze the etiologies of G6PD deficiency in neonates with hyperbilirubinemia in the Zunyi region with the aim of providing scientific evidence for the clinical diagnosis and treatment. For the gene detection, 64 neonates with hyperbilirubinemia were selected as the observation group and 30 normal neonates were selected as the control group, and the risk factors for hyperbilirubinemia were investigated by using multivariate logistic regression analysis. Among the neonates in the observation group, 59 cases had the G1388A mutation (92.19%) and 5 cases had the G1376T mutation (7.81%). No mutation was detected in the control group. In the observation group, the proportion of neonates who were born prematurely, with artificial feeding, with the age of starting feeding of more than 24 h, the time of first bowel movement of more than 24 h, premature rupture of membranes, infection, scalp hematoma, and perinatal asphyxia was higher than that in the control group, and the difference was statistically significant (p< 0.05). Multivariate logistic regression analysis showed that prematurity, infection, scalp hematoma, perinatal asphyxia, the age of starting feeding of more than 24 h, and the time of first bowel movement over 24 h were risk factors for the development of neonatal hyperbilirubinemia (p< 0.05). The G1338A and G1376T mutations were important features of the genetics of neonatal hyperbilirubinemia, and genetic detection together with the prevention of prematurity, infection, scalp hematoma, perinatal asphyxia, the age of starting feeding, and the time of first bowel movement would help reduce the incidence of this disease.