Objective To explore the relationship between suicidal ideation and SLC6A4 gene methylation in children and adolescents with pediatric bipolar disorder （PBD） and depressive episodes. Methods From December 2020 to December 2022， 43 patients with PBD and depressive episodes in the Department of Clinical Psychology of Xinjiang Uygur Autonomous Region People's Hospital were selected as the research subject. The suicidal ideation of patients was evaluated using the Self-rating Idea of Suicide Scale （SIOSS）. Patients with a total score of ≥ 12 and a concealment factor score of ＜ 4 were included in the suicidal ideation group （n=29）， and patients with a total score of ＜ 12 were included in the non-suicidal ideation group （n=14）. Methprimer software was used to predict methylation islands and design methylation primers in the SLC6A4 gene promoter region. The extracted DNA was transformed by sulfite for PCR amplification and pyrophosphate sequencing to determine the methylation CpG site and methylation rate. This study compared the differences in methylation at different sites of the SLC6A4 gene between two groups of patients， and adopted Spearman correlation to analyze the correlation between gene methylation and suicidal ideation. Results Gene methylation testing showed that the methylation sites of the SLC6A4 gene in both groups of patients included CpG1， CpG2.3， CpG4， and CpG5.6 sites. Comparison of gene methylation rates at CpG1， CpG2.3， and CpG4 sites in patients in the suicidal ideation group and the non-suicidal ideation group ［48.28% （14/29） vs 8/14， 96.55% （28/29） vs 14/14， 20.69% （6/29） vs 6/14］ ， the differences were not statistically significant （χ2 =0.297， 0.494， 2.306； P ＞ 0.05） . The rate of gene methylation at the CpG5.6 site was higher in patients in in the suicidal ideation group than in the non-suicidal ideation group ［68.97% （20/29） vs 5/14］ ， and the difference was statistically significant （χ2 =4.289， P ＜ 0.05）. Correlation analysis showed that suicidal ideation in patients with PBD and depressive episodes was not correlated with CpG1， CpG2.3， or CpG4 site methylation in the SLC6A4 gene （r=-0.244， -0.210， -0.281； P ＞ 0.05）， but was positively correlated with CpG5.6 site methylation， and the difference was statistically significant （r=0.312， P＜ 0.05）. Conclusions The suicidal ideation of patients with PBD and depressive episodes is related to the SLC6A4 gene methylation at CpG5.6 site， providing a basis for clarifying the causes of suicidal ideation.