Objective This study aimed to evaluate the associations of serum folate and/or vitamin B-12 concentrations with obesity among Chinese children and adolescents. Methods A cross-sectional study was conducted including 3,079 Chinese children and adolescents, aged 6 to 17 years, from Jiangsu, China. Anthropometric indices, such as, children's body mass index (BMI), BMI z -scores, waist circumference, and waist -to -height ratio were utilized. Multivariable linear regression and generalized additive models were used to investigate the associations of serum folate and vitamin B-12 levels with anthropometric indices and odds of obesity. Results We observed that serum vitamin B-12 concentrations were inversely associated with all anthropometric indices and the odds of general obesity [odds ratio ( OR ) = 0.68; 95% confidence interval ( CI ) = 0.59, 0.78] and abdominal obesity ( OR = 0.68; 95% CI = 0.60, 0.77). When compared to participants with both serum vitamin levels in the two middle quartiles, those with both serum folate and vitamin B-12 levels in the highest quartile were less prone to general ( OR = 0.31, 95% CI = 0.19, 0.50) or abdominal obesity ( OR = 0.46, 95% CI = 0.31, 0.67). Conversely, participants with vitamin B-12 levels in the lowest quartile alongside folate levels in the highest quartile had higher odds of abdominal obesity ( OR = 2.06, 95% CI = 1.09, 3.91). Conclusion Higher serum vitamin B-12 concentrations, but not serum folate concentrations, were associated with lower odds of childhood obesity. Children and adolescents with high levels of vitamin B(12 )and folate were less likely to be obese.