Gestational diabetes mellitus (GDM) is a complex disease induced by a combination of genetic factors and environmental exposures. Growing evidence suggests that common single nucleotide polymorphisms within miRNA-binding sites (miR-binding SNPs) contribute to the development of various diseases. However, the roles of miR-binding SNPs in GDM have not been fully elucidated. The CDKN2A/B genes have been identified as two of the strongest genetic determinants for diabetes risk. The aim of the study was to first investigate the associations between miR-binding SNPs of CDKN2A/B, GDM susceptibility, and quantitative metabolism traits.Three miR-binding SNPs of CDKN2A/B gene (rs1063192, rs3217992, and rs3088440) were selected and genotyped using TaqMan allelic discrimination assays in 839 cases of GDM and 900 controls.The CC genotype of CDKN2B rs1063192, which is located in the hsa-miR-323b-5p binding site, was significantly associated with GDM [OR 1.418 (1.143, 1.908); p = 0.003]. The C allele of rs1063192 occurred with significantly higher frequency in GDM [OR 1.22 (1.03, 1.44); p = 0.021]. The rs1063192 genotype CC exhibited increased glucose levels at 1 h and 3 h, as well as higher insulin levels at 3 h during an OGTT compared with the control TT genotype (p < 0.05). We also found that the rs1063192 CC genotype was associated with lower total cholesterol and LDL cholesterol levels (p < 0.05).The CC genotype of CDKN2B rs1063192 in the hsa-miR-323b-5p binding site increased the risk of GDM in pregnant Chinese Han women. Importantly, our study provides evidence that miR-binding SNPs are a novel source of GDM susceptibility loci.