Monogalactosyl diacylglycerol (MGDG) is an important component of plant photosynthetic membranes and plays a regulatory role in the resistance of plants to adverse conditions. The genome of MGDG gene family (GhMGDs) of Gossypium hirsutum L. were analyzed and identified by bioinformatics method, and verified its expression rule under abiotic stress in this study. The results showed that: (1) There were 17 members of this gene family in the upland cotton genome, the amino acid residues ranged from 435 aa to 888 aa, the heoretical isoelectric point ranged from 6.00 to 9.67, and all genes contain 6-8 introns. (2) According to the phylogenetic tree, this gene family can be divided into type A and type B MGDG synthetase. The gene structure and conserved motifs of each member of each subfamily were very similar. (3) The 17 MGDG genes were unevenly distributed on 7 chromosomes. The secondary structures showed that the family was mainly composed of α-helix and random coil. (4) The results of qRT-PCR analysis showed that the expression analysis of MGDG gene family members were the difference in the expression levels of each MGDG gene in four different tissues of Upland cotton. GhMGD2, GhMGD12 and GhMGD16 genes were highly expressed in upland cotton roots. GhMGD7, GhMGD9 and GhMGD10 genes were highly expressed in upland cotton leaves. Furthermore, we identified six candidate gene expression patterns induced by low phosphorus stress, including GhMGD2, GhMGD7, GhMGD9, GhMGD10, GhMGD12 and GhMGD16. The expression of GhMGD2 gene at 72 h under low phosphorus treatment was 72 times that of suitable phosphorus treatment.