Background: Around the world, especially in aerobic soils, because the solubility of iron (Fe) is very low, plants are often stressed by low Fe tress, and the growth, yield, and quality of crops will be inhibited in the case of severe Fe deficiency. The metabolism of Fe in plants is controlled by a series of complex transport, storage, and regulatory mechanisms to maintain the homeostasis of Fe in cells. Allohexaploid wheat (Triticum aestivum L.) is an important food crop and is more sensitive to low Fe tress. Although some studies have been conducted on the low Fe tress response of different plant species, these mechanisms are still unclear in wheat. Results: According to the results of transmission electron microscope, and paraffin section, under low Fe stress, leaf chlorosis was due to damage to the chloroplast structure, and the effect on root structure was mediated by reducing the rate of cell division in meristems and reducing cell elongation in the elongation zone. ICP-MS showed that low Fe stress significantly limited the absorption of essential elements, including N, Pi, K, Ca, Mg, Fe, Mn, Cu, Zn, and B nutrients. RNA sequencing revealed the transcriptomic changes of wheat under low Fe stress. The results showed that 378 and 2,619 differentially expressed genes (DEGs) were identified in the shoots and roots, respectively. These DEGs were mainly involved in the synthesis of Fe chelating agents, ion transport, photosynthesis, amino acid metabolism, protein synthesis, and other processes. Next, to find the core genes responding to low Fe stress, the gene co-expression network diagram was constructed. The results indicated that TaIRT1b-4A, TaNAS2-6D, TaNAS1a-6A, TaNAS1-6B, and TaNAAT1b-1D might play a key role in dealing with low-Fe stress. Conclusions: These research results might help to fully understand the morphological and molecular responses of plants to low Fe stress, and provide excellent genetic resources for the genetic modification of Fe deficiency crops.