Waterlogging poses a major challenge to Welsh onion (Allium fistulosum L.) production, exacerbated by climate change-induced extreme weather. Unraveling the molecular mechanisms of waterlogging tolerance is essential for breeding resilient cultivars. Here, we compared two Welsh onion varieties: BJQC (tolerant) and YZDC (sensitive). Waterlogging treatment revealed that YZDC exhibited higher accumulation of reactive oxygen species (ROS), including hydrogen peroxide (H₂O₂), superoxide ions (O₂^–·), and malondialdehyde (MDA), leading to increased mortality. In contrast, BJQC demonstrated enhanced waterlogging tolerance, which was attributed to its ability to upregulate flavonoid biosynthesis genes, resulting in higher flavonoid accumulation under waterlogging stress. Transcriptomic analysis identified that the activation of flavonoid pathway-related genes in BJQC was central to this response. In addition, genes associated with jasmonic acid and gibberellin signaling were activated. Weighted gene co-expression network analysis (WGCNA) revealed that WRKY31 and MATE likely played critical roles in regulating flavonoid biosynthesis under waterlogging conditions. Genome-wide association study (GWAS) results from natural populations further supported the significance of these genes in waterlogging tolerance. Our comprehensive multi-omics analysis, including phenotypic, physiological, transcriptomic, and genomic approaches, provided new insights into the molecular mechanisms underlying Welsh onion responses to waterlogging. These findings highlight WRKY31 and MATE as key candidates for improving waterlogging tolerance in crop breeding programs.