Objective To investigate the variation of genes related to neonatal hyperbilirubinemia jaundice and the diseases caused by hyperbilirubinemia jaundice, and its distribution in different degrees of jaundice. Methods A total of 167 neonates diagnosed with hyperbilirubinemia in NICU from July 2022 to July 2023 were selected and divided into severe and non-severe jaundice groups. Gene detection was performed by high-throughput second-generation gene sequencing technology. The jaundice gene variants were rated as pathogenicity, and the positive, carrying and negative rates of jaundice gene variants in children were analyzed, and the distribution of jaundice gene variation and related diseases in the two groups were also analyzed. Results Among 167 children, 18 cases (10.8%) were positive for jaundice gene variation, 55 cases (32.9%) were carriers, and 94 cases (56.3%) were negative. There were 8 genes involved in UGT1A1, ATP7B, HBB, SLC25A13, ATP8B1, SMPD1, G6PD and SLC10A1, among which the mutation frequency of UGT1A1 gene was up to 45.32%, and c.211G>A was the high frequency mutation site. In the group of 31 children with severe jaundice, 16 (51.6%) had positive results for jaundice gene mutations, and all 15 cases of Gilbert syndrome/Crigler-Najjar syndrome had UGT1A1 gene mutations. Among the 136 non-severe jaundice patients, only 2 cases (1.47%) were positive, and 1 case of Gilbert syndrome / Crigler-Najjar syndrome had a variation in UGT1A1 gene. Comparing the rates of positive, carrying and negative of jaundice gene variation between the two groups, the results showed that the positive rate of severe jaundice group was significantly higher than that of non-severe jaundice group, and the negative rate was significantly lower than that of non-severe jaundice group, with statistical significance (P<0.014). Conclusions Jaundice gene variation is closely related to the occurrence and severity of neonatal hyperbilirubinemia. The common cause is UGT1A1 gene variation, and c.211G>A is the high frequency mutation site. It is of great clinical significance to conduct gene detection for children with hyperbilirubinemia, especially severe hyperbilirubinemia.