Abstract: Flooding is one of the most devastating abiotic stresses in agriculture, and enhancing flood tolerance is critical for sustainable crop production. Soybean (Glycine max) is highly susceptible to flooding stress. However, the molecular mechanism underlying soybean response to flooding stress remains largely unknown, and the genes available for improving soybean flood tolerance are relatively limited. In this study, we characterized the function of the predicted cytochrome P450 gene, GmSUR2a, in regulating submergence tolerance in both soybean and Arabidopsis. The Arabidopsis SUR2 gene played a positive role in regulating submergence tolerance. The GmSUR2a, which localizes to a previously identified quantitative trait locus (QTL) for waterlogging tolerance on soybean chromosome 03, shared conserved functions with AtSUR2 in regulating submergence tolerance. Transgenic soybean plants overexpressing GmSUR2a displayed enhanced submergence tolerance accompanied by reduced auxin levels. Further experiments revealed that auxin negatively regulates submergence tolerance: Exogenous auxin application decreased survival rates, and auxin signaling mutants exhibited improved tolerance. We also identified that GmAGL15 transcription factor directly repressed GmSUR2a expression. Importantly, field trials confirmed that GmSUR2a overexpression not only improved submergence tolerance but also increased the yield of transgenic soybean plants. Our findings provide new insights into the molecular mechanisms of submergence tolerance and establish GmSUR2a as a promising target for breeding flood-resistant soybean varieties.