Engineering karyotypes could expand the genetic and breeding potential of crops, but restructuring gigabase-scale polyploid genomes remains challenging. Here, we develop centromere editing-mediated chromosomal variation, a strategy using CRISPR-Cas9 to target abundant centromeric retrotransposons in hexaploid wheat. Centromere editing-mediated chromosomal variation efficiently induces simultaneous chromosome cleavage across the genome, generating diverse karyotypic variants and reconfiguring up to 11 chromosomes in one generation. Notably, it produces widespread reciprocal translocations, with one line carrying six events involving seven chromosomes. Newly formed translocation chromosomes undergo centromere remodeling, enabling their relatively stable maintenance and heritable transmission. Moreover, balanced translocations impose minimal transcriptional perturbation and maintaining normal growth. These results establish centromeres as effective sites for chromosome engineering breeding and provide a scalable framework for karyotype redesign in polyploid crops.