Membrane lipid remodelling is one of the strategies that plants have developed to combat abiotic stress. In this study, physiological, lipidomic and proteome analyses were conducted to investigate the changes in glycerolipid and phospholipid concentrations in the wheat (Triticum aestivum L.) cultivars CIGM90.863 and Seri M82 under hypoxia treatment. The growth of CIGM90.863 remained unaffected, whereas Seri M82 was significantly stunted after 8 days of hypoxia treatment. The concentrations of all lipids except lysophosphatidylglycerol were significantly higher in the leaves of Seri M82 than in CIGM90.863 under normal growth conditions. The lipid profile changed significantly under hypoxia stress and varied between genotypes for some of the lipids. Phosphatidic acids remained unchanged in Seri M82 but they were gradually induced in CIGM90.863 in response to hypoxia stress because of the higher phospholipase D expression and lower expression of diglycerol kinase and phosphatidate phosphatases. In contrast, digalactosyldiacylglycerol content was highly stable in CIGM90.863 following hypoxia treatment, although it decreased significantly in Seri M82. Phosphatidylglycerol and lipoxygenase showed a stronger and faster response in CIGM90.863 than in Seri M82 under hypoxia stress. Different membrane lipid adjustments in wheat under oxygen deficiency conditions could be partly responsible for the differing tolerance of Seri M82 and CIGM90.863. This study will help us to better understand how wheat tolerates hypoxia stress by regulating lipid remodelling.