The current study aims to explore a noninvasive molecular marker that can evaluate the therapeutic effect and prognosis of gestational diabetes mellitus (GDM). Differentially expressed miRs were identified using microarray assay and the findings were verified using RT-PCR. Receiver operating characteristic (ROC) was performed to explore the diagnostic value of serum and urine miR-429 in GDM women. The relationship between miR-429 and homeostatic model assessment-insulin resistance (HOMA-IR) was analyzed using Pearson's correlation assay. Dual luciferase assay and western blot were carried out to explore the possible target gene of miR-429. Microarray assay and RT-PCR showed that miR-429 was found to be significantly increased in both serum and urine samples of GDM women compared with those of normal blood glucose pregnancy group (NGT). Also, the expression of miR-429 in serum and urine was positively correlated with HOMA-IR. ROC analysis showed that both serum and urine miR-429 could screen GDM from NGT. Furthermore, dual luciferase reporter and western blot assay indicated that insulin receptor substrate- (IRS-) 1 was a target gene of miR-429. In summary, the increase of serum and urine miR-429 level is a risk factor of insulin resistance in pregnant women with GDM.