Polyploidization is a fundamental evolutionary process in plants, including bread wheat. In the present study, we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58 (AK58), a modern elite polyploid wheat cultivar with a recently released reference genome, and in other wheat genomes, including landraces, synthetic wheat, and several breeding lines. Over 40% of transposable element (TE) families exhibit biased distribution across the three wheat subgenomes. Approximately 95.0% (113 421) of genes are co-located with TEs, and these variable TEs significantly contribute to homoeologous divergence. We found that about 80% of triad homoeologs are divergent due to differences in expression or sub-functionalization. In addition, subgenome divergence potentially promote polyploid wheat domestication and improvement by increasing favorable homoeoallele combinations. Our findings suggest that homoeolog divergence contributes to the adaptation, domestication, and improvement of hexaploid wheat. The contribution of subgenomic divergence to polyploid heterosis is also discussed. This study provides a valuable resource for the investigation of how TEs drive homoeologous divergence during wheat domestication and improvement.