Objectives　To explore the association between the single nucleotide polymorphism (SNP) rs2239669 in makorin ring-finger protein 3 (MKRN3) gene and the susceptibility to central precocious puberty (CPP). Methods　A case-control study including 246 children with CPP and 269 healthy children was performed. The genotype and MKRN3 expression levels of patients were analyzed by PCR-HRM and RT-PCR，respectively. Results　SNP rs2239669 genotype (TT，TC，CC) and allele frequencies (T and C) were different between cases and controls，with higher CC genotype in CPP patients. Under recessive model (CC/TT+TC)，CC genotype was higher in CPP group and associated with higher risk of CPP (95%CI：1.062-2.143， P=0.021). MKRN3 expression levels were different among patients with different genotypes，of which TT genotype had the highest level followed by TC and CC (0.376±0.094, 0.330±0.068, 0.250±0.072， P=0.041). Conclusions　MKRN3 SNP rs2239669 was associated with increased risk of CPP, and patients with TT genotype had higher MKRN3 levels.