Polyploidization is a major driving force for evolutionary innovation and environmental adaptation in plants and is notably prevalent in kiwifruits. However, the molecular mechanisms through which subgenome interactions influence vigor and stress resilience remain largely unclear. Here, the high-quality genome of the tetraploid kiwifruit Actinidia valvata, which exhibits strong waterlogging tolerance compared to cultivated varieties is reported. The analysis reveals that the polyploid genome is of hybrid origin and exhibits subgenome dominance. The enhanced gene expression in the dominant subgenome is accompanied by fewer transposable elements, lower DNA methylation levels, increased chromatin accessibility, and biased global RNA m(6)A methylation abundance and distribution. It is demonstrated that this dominance is established, in part, prior to polyploidization. The dominant subgenome is transcriptionally more responsive to waterlogging stress, consistent with the fact that its putative progenitor is also waterlogging tolerant, affirming the significant role of the dominant subgenome in mediating waterlogging tolerance in A. valvata. Furthermore, inhibition of RNA m(6)A methylation in A. valvata roots enhances their activity under waterlogging stress, while waterlogging modulates m(6)A modifications, particularly in the dominant subgenome, affecting genes known to be involved in waterlogging responses. These findings reveal that subgenome dominance in A. valvata operates through multiple regulatory mechanisms, collectively endowing the polyploid with unique traits inherited from its progenitors.