Polyploidy is a significant driving force for the evolution and diversification of angiosperms. Numerous researches on the genomic and transcriptomic analyses of polyploidy have been conducted to decipher the molecular mechanism underlying the success of polyploidy. However, mRNA regulation at the posttranscriptional level is rarely conducted in polyploidy. Among the posttranscriptional processes, RNA degradation is an active and critical process that dictates RNA levels and, in part, controls the relative levels of gene expression. Here, we obtained the mRNA decay landscape in durum wheat (T. turgidum ssp. durum, BBAA). The mRNA decay landscape revealed subgenome asymmetry at the mRNA stability, contributing to the steady-state mRNA abundance. Notably, mRNAs undergoing miRNA-mediated decay showed an overall faster decay rate than other mRNAs. Interestingly, the miRNA-mediated decay also displayed subgenomic asymmetry, although the complementarity between miRNA and target sites remains mainly identical between the two subgenomes. Further analysis uncovered that RNA structure features are prevalently associated with mRNA decay rates where weak RNA structures, particularly in the 3’UTR regions, are significantly associated with fast mRNA decay. We further found that the RNA structure difference in the 3’UTR regions between the two subgenomes is significantly associated with the subgenomic differential mRNA decay rates. Interestingly, some SNVs in the 3’UTR between subgenomes could induce significant structure disparities, significantly contribute to the RNA structure divergences. Further validations demonstrated that these SNVs were likely to be selected during human breeding to achieve the divergence of mRNA decay between subgenomes and, consequently, the subgenomic difference of mRNA levels. Our study provides a new perspective of post-transcriptional regulation of gene expression for wheat genetic research and, more generally, for polyploid crop breeding in the future.