ABSTRACT Aims/Introduction The aim of the study was to investigate the association of single nucleotide polymorphisms, haplogroups, and copy number in the D‐loop region of mitochondrial DNA (mtDNA) with the genetic susceptibility to gestational diabetes mellitus (GDM) and postpartum abnormal glucose metabolism (AGM). Materials and Methods This was a case–control study in which peripheral blood samples were collected from 500 GDM patients and 500 normal pregnant women from 14 to 20 weeks of pregnancy. The sequence of the D‐loop region of mtDNA was detected by Sanger sequencing, and the copy number of mtDNA was detected by qPCR. Results Analysis of SNPs in the D‐loop region of mtDNA showed that 249d was a risk factor and 309+C and 16193+C were protective factors for GDM. The mtDNA haplogroups R9 and M* were a risk factor and protective factor for GDM, respectively. Compared to the group with normal postpartum glucose tolerance, the haplogroups M7b and N9a were associated with an increased risk of AGM. The whole blood mtDNA copy number was lower in the GDM group than in the control group and was also lower in the postpartum AGM group than in the postpartum normal group. The plasma free mtDNA copy number was higher in the GDM group than in the control group, and higher in the postpartum AGM group than in the normal postpartum group. Conclusions Mitochondrial genomic variants are associated with the risk of GDM and postpartum AGM, and may provide some etiologic evidence for GDM and postpartum AGM.