Objective: To assess the associations between the single nucleotide polymorphism (SNP) rs 12225230 of salt inducible kinase 3 ( SIK 3) and obesity/central obesity in children, and to provide evidence for screening intervention for obesity in children and adolescents. Methods: A cluster sampling of 2 030 children aged 7-18 years in Beijing were enrolled and height, weight and waist circumference were measured according to the manufacturer. The genotype frequency of SNP rs 12225230 was detected by matrix assisted laser analysis/ionization time of flight mass spectrometry (MALDI TOF MS). Logistic regression and multiple linear regression were applied to analyze the associations between SNP rs 12225230 and overweight/obesity and central obesity. Polyphen2 database was used to predict the effect of SNP rs 12225230 on the protein function of SIK 3. GTEx database was used to explore expression quantitative trait loci (eQTL) of SNP rs 12225230. Results: C allele of SNP rs 12225230 was a risk allele for obesity and severe obesity in children ( OR obesity =1.50, 95% CI=1.10-2.04, P =0.01; OR severe obesity =1.72, 95% CI=1.23-2.39, P <0.01). The SNP rs 12225230 was positively associated with waist circumference and waist height ratio ( β waist circumference =1.40, 95% CI=0.28- 2.52 , P =0.01; β waist height ratio =0.01, 95% CI=0.00-0.02, P =0.01). C allele of SNP rs 12225230 may be harmful to the function of the protein encoded by the SIK 3, and was positively related to the expression of the APOA 1 in the heart tissue. Conclusion SNP rs 12225230 is associated with obesity and central obesity in children, and SNP rs 12225230 may affect the expression of the APOA 1 in children, but its association with lipid metabolism needs to be verified