Premature ejaculation (PE) is a common male sexual dysfunction disorder, and is considered to have the genetic predisposition. However, the internal regulation mechanisms is still unclear. Hence, this study intended to explore the effects of genetic polymorphisms of CYP24A1 on the risk of PE. This case–control study genotyped three SNPs of CYP24A1 (rs2762934, rs1570669 and rs6068816) from 139 PE patients and 372 healthy men using Agena MassARRAY platform. Collected data was then processed in SPSS 18.0. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in logistic regression analysis to evaluate the associations between CYP24A1 polymorphisms and the PE risk. The results suggested that allele A of rs1570669 was significantly associated with the increased PE risk (OR=1.38, 95% CI=1.04–1.84, P=0.026). Meanwhile, we also identified rs1570669 as a risk factor of PE under the additive model(OR=1.47, 95% CI=1.02–2.11, P=0.039) by comparing the genotypic distributions between cases and controls, and genotype AA of rs1570669 was detected to be significantly related with an increased risk of PE under the codominant model (OR=2.26, 95% CI=1.06–4.83, P=0.036). This study is the first to proved that the genetic variants of CYP24A1 played essential role in affecting the susceptibility to PE in Chinese Han.