<b><i>Background:</i></b> Previous studies have demonstrated the close relationship between vitamin D, vitamin D receptor (VDR), and obesity. Nevertheless, few studies have reported wherther the relationship among these is associated with the risk of cardiovascular diseases (CVDs) in Chinese children and adolescents. <b><i>Objective:</i></b> The present study aimed to reveal the effects of obesity, serum vitamin D levels, and VDR <i>FokI</i> genotype on the risk of CVDs in children and adolescents in Sichuan, China. <b><i>Methods:</i></b> Children and adolescents were recruited into a cross-sectional study. Serum vitamin D levels, serum lipid levels, and VDR <i>FokI</i> gene polymorphisms were measured in the laboratory. The selected lipid factors were used as biomarkers of CVD risk. The impact of obesity, vitamin D levels and VDR <i>FokI</i> genotype on CVD risk factors were investigated. <b><i>Results:</i></b> Higher lipid levels were observed in children and adolescents in the obese group, when compared to the nonobese group. In the obese group, the C allele carriers had significantly lower concentrations of lipids, when compared to the TT genotype. C allele carriers who were vitamin D deficient had lower levels of total cholesterol (TC), triglycerides (TG), apolipoprotein B (Apo-B), total cholesterol/high-density lipoprotein cholesterol (TC/HDL-C), low-density lipoprotein cholesterol/high-density lipoprotein cholesterol (LDL-C/HDL-C), and triglycerides/high-density lipoprotein cholesterol (TG/HDL-C), when compared to those with the TT genotype in obese children and adolescents. For vitamin D-insufficient obese children and adolescents, the TC, Apo-B, and TC/HDL-C in the C allele carriers were significantly lower, when compared to those in the TT genotype in obese children and adolescents. <b><i>Conclusion:</i></b> Obese children with low vitamin D levels, who are carriers of the C allele of the <i>FokI</i> gene, have lower levels of several biochemical markers of CVD risk, when compared to those who were TT homozygous. Obese children and adolescents may benefit from vitamin D supplementation, terms of lowering their CVD risk, particularly when they are carriers of the C allele of the <i>FokI</i> gene.