Food shortages are one of the most serious global problems in this century and it is important to increase the food production. Soybean is one of the important crop in the world, which is a source for protein, vegetable oil, and phytochemicals. On the other hand, global climate changes influence the magnitude and frequency of hydrological fluctuations and cause unfavorable environment for plant growth and development. Soybean is sensitive to flooding stress, which markedly reduces its growth. To identify the mechanism of flooding tolerance at initial stage in early-stage soybean, proteomic, transcriptomic, and metabolomic techniques were used. Flooding tolerant mutant line and abscisic acid-treated soybean, which exhibited flooding tolerant phenotype, were used as materials. Early-stage soybeans were treated during initial stage of flooding stress and roots were collected for proteomic as well as metabolomic and transcriptomic analyses. Data were analyzed using functional categorization, cluster separation, and in silico protein-protein interaction. Furthermore, commonly changed metabolites, proteins, and genes between mutant and abscisic acid-treated soybeans were considered as flooding-tolerance related candidate factors. Finally, omics results were integrated to analyze the flooding tolerant mechanism in soybean and confirmed using biochemical and biological techniques. These results suggest that flooding tolerance at initial stage in early-stage soybean might be through protecting newly synthesized proteins and enhancing activities of antioxidative enzymes to remove reactive oxygen species. Furthermore, an integrated approach of proteomics and computational genetic modification effectiveness analysis was applied to explore flood-tolerant genes in soybean, suggesting that proteins related to energy metabolism might play an essential role to confer flood tolerance in soybeans.