Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potentiates their spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. We identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (ca. 193 Mb) and 4A (ca. 167 Mb) were reciprocally translocated. Five homogeneous translocation lines were developed by selfing of the founder plant, including both unbalanced and balanced types. We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We show that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induce substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifest clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines show immediate enhanced reproductive fitness relative to wild-type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with phenotypic and metabolic consequences that are likely relevant to polyploid evolution and crop breeding.