Oxidative stress plays an important role in the pathophysiology of gestational diabetes mellitus (GDM). We investigated the relationship between NADPH oxidase p22phox subunit (CYBA) C242T (rs4673) and myeloperoxidase (MPO) G-463A (rs2333227) genetic variants and GDM in 719 patients with GDM and 1205 control women. Clinical, metabolic, and oxidative stress parameters were analyzed. We found that frequencies of the A allele (15.6% vs. 12.3%) and GA + AA genotype (28.5% vs. 23.2%) of the MPO G-463A variation were significantly higher in patient with GDM than in the control women (OR = 1.318, 95% CI: 1.068–1.625, P = 0.010 for the dominant model; OR = 1.999, 95% CI: 1.040–3.843, P = 0.034 for the recessive model; OR = 1.320, 95% CI: 1.095–1.591, P = 0.004 for the allele model). Genotype GA + AA remained a significant predictor of GDM in a logistic regression model including age and BMI at delivery (OR = 1.282, 95% CI: 1.037 ‒ 1.583, P = 0.021). Furthermore, the -463A allele was associated with higher TG and the 242T allele was related to higher pre-pregnancy BMI and oxidative stress index in all subjects (P <0.05). The 242T allele was also associated with higher HOMA-IR but lower serum total antioxidant capacity in patients with GDM (P <0.05). We conclude that the MPO G-463A, but not the CYBA C242T, genetic variation, is associated with an increased risk of GDM in Chinese women. These two genetic polymorphisms may be linked to obesity, dyslipidemia, insulin resistance, and oxidative stress.