Genomic shock refers to the various responses of the genome when faced with challenges, which can be observed through rapid genomic rearrangements, genome downsizing, and intergenomic invasion. One common manifestation of genomic shock is an imbalance in the epigenetic control of transposons (TEs), leading to their rapid proliferation. It is important to investigate whether this surge also affects the centromeres, which are heavily populated by TEs. In order to understand the dynamic response of functional centromeres during polyploidization, we synthesized a series of diploid, tetraploid, and hexaploid Triticum-Aegilops species complex lines and subjected them to multiple generations of self-crossing. By closely examining the detailed layout of the centromeric environment, we observed that the loading of CENH3, a centromere-specific histone variant, remained stable during the successive processes of hybridization, genome doubling, and limited selfing in all the resynthesized polyploid lines. Our findings demonstrate that the dynamics of centromeres in individual Triticum taxa respond gradually to genomic shocks and highlight that the progressive evolution of centromere CENH3 in the initial generations of synthetic allopolyploid wheat is a universal phenomenon that ensures the stability of the early genome in allopolyploids and provides a foundation for subsequent centromere evolution.