Objective To analyze the clinical and genetic variation characteristics of hereditary epilepsy in neonates and explore the correlation between the characteristics of genetic variations and clinical manifestations. Methods A retrospective collection was made of neonatal hereditary epilepsy cases admitted to Hebei Children's Hospital from January 2019 to December 2024. The cases were divided into KCNQ2 group and non-KCNQ2 group based on the results of gene sequencing. The clinical features of the two groups were compared, and the genotype-phenotype correlation of KCNQ2 was analyzed. Results A total of 43 cases of neonatal hereditary epilepsy were included, including 26 boys and 17 girls, with a gestational age of 39.4 (38.1-40.3) weeks and a birth weight of 3400 (3000-3400) g. There were 24 cases in the KCNQ2 group and 19 cases in the non-KCNQ2 group. The onset time of epilepsy was 3.0 (2.0-7.0) days after birth, which was earlier in the KCNQ2 group than in the non-KCNQ2 group (P<0.05). The main seizure forms were clonic (62.8%) and tonic (53.5%) seizures. The main abnormality on head MRI was abnormal brain parenchymal signal (72.1%). The most common finding on video electroencephalogram was multifocal discharges (34.9%). There were no statistically significant differences between the two groups (P>0.05). In the KCNQ2 group, there were 13 cases of self-limiting neonatal epilepsy (SeLNE) and 11 cases of developmental and epileptic encephalopathy (DEE). Among the 23 cases successfully followed up, 19 cases had seizure control, 8 cases had significant developmental delay, and 2 cases died. In the non-KCNQ2 group, there was 1 case of SeLNE, 10 cases of DEE, and 8 other cases. Among the 13 cases successfully followed up, 7 cases had seizure control, 7 cases had significant developmental delay, and 4 cases died. The proportion of SeLNE in the KCNQ2 group was higher than that in the non-KCNQ2 group (54.2% vs. 5.3%, P<0.01), and the proportion of death and significant developmental delay was lower in the KCNQ2 group (43.5% vs. 84.6%, P=0.033). There were 19 cases of KCNQ2 nucleotide sequence variations, including 10 cases of SeLNE, 5 cases of hereditary variations, and 4 cases of missense variations. Seven amino acid changes were located at the C-terminal. All 9 cases of DEE were de novo variations, including 7 cases of missense variations, and 5 amino acid changes were located at the S4, S6 and adjacent regions, and the B-helix region. Prediction of protein structural changes induced by 11 missense variants: among 4 SeLNE cases, 2 showed alterations in protein secondary structure, 3 exhibited changes in hydrogen bonds, and 4 demonstrated decreased protein stability; among 7 DEE cases, 6 displayed alterations in protein secondary structure, 4 presented changes in hydrogen bonds, and 6 manifested decreased protein stability. Conclusions KCNQ2 gene variations are the most common in neonatal hereditary epilepsy. Compared with other gene variations, KCNQ2-induced neonatal epilepsy has an earlier onset time and a lower proportion of adverse outcomes. Among them, de novo, missense, and variations at important functional domain sites, may be associated with severe phenotypes of DEE.