Spike development of wheat line 3558M with multiple phenotypes, including fewer tillers, delayed floral transition, and death of the shoot apical meristem was strongly inhibited by low temperature stress in spring. We systematically investigated the genes and pathways underlying the differences using ITRAQ proteomics and RNA-sequencing technologies and found multiple biological pathways including to the cold acclimation pathway and multiple defence responses (e.g. reactive oxygen species-mediated hypersensitive response, salicylic acid-mediated systemic acquired resistance) are activated and led to tillers death of the wheat line 3558M under cold stress. Multiple MADS-box genes and the SVP-SCO1-LFY flowering pathway were significant downregulated to delay the floral transition. Particularly, two TaPIN proteins were significantly downregulated, and multiple auxin transport proteins and auxin signalling genes were also differentially expressed. Meanwhile, the auxin content in the site of axillary buds of 3558M