Due to the influence of geography and climate, waterlogging severely limits the high and stable yield of wheat. Under low oxygen stress caused by waterlogging, wheat roots are induced to form aerenchyma. In this study, two wheat varieties, Huamai 8 and Huamai 9, were subjected to waterlogging treatments. After 12 hours treatment, autophagy was observed in root elongation zone by transmission electron microscope in Huamai 8. With the prolongation of the treatment, the nuclear membrane dissolves in the nucleus, and the nucleolus disappears while the endoplasmic reticulum is gradually broken and arranged disorderly. At 48 hours under waterlogging, Huamai 8 showed longer root length and larger aerenchyma area when compared to Huamai 9. These results demonstrated that the morphogenesis of aerenchyma is accompanied by autophagy and PCD. In addition, Huamai 8 showed better waterlogging resistance than Huamai 9. Transcriptome analysis revealed that genes involved in multiple metabolic pathways were distinctively regulated between Huamai 8 and Huamai 9, such as hormone signaling, amino acid metabolism, glycolysis and TCA cycle. Hormone profiling showed that auxin and JA might be involved in aerenchyma formation. Together, our results provided novel insights into cellular and molecular adaptation under waterlogging stress in wheat.