Association between vitamin D receptor (VDR) genetic polymorphism and obesity was observed in several case-control studies. This study hypothesized that these associations could be verified in family-based study. We aimed at investigating the associations between VDR SNPs and obesity (BMI ≥ 28 kg/m2) by case-control study with 688 subjects and family-based study with 419 pedigrees. The results of case-control study suggested that rs3847987 (AC vs CC, Adjusted OR: 1.938, 95% CI: 1.359-2.763, P = 0.000405) was associated with obesity. Allele C of rs3847987 was risk factors for obesity (P = 0.006). Furthermore, association of rs3847987 with BMI was verified in family-based study (Z = 2.077, P = 0.037811). In addition, sibling with AC genotype of rs3847987 had significant higher BMI than CC genotype in the same family (P = 0.03). Therefore, it could be concluded that VDR genetic polymorphism (rs3847987) may be associated with obesity.