Beef from Japanese Black cattle (Japanese Wagyu) is renowned for its flavor characteristics. To clarify the key metabolites contributing to this rich and sweet aroma of beef, an omics analysis combined with GC-olfactometry (GC-O) and metabolomics analysis with gas chromatography-mass spectrometry (GC-MS) were applied. GC-O analysis identified 39 odor-active odorants from the volatile fraction of boiled beef distilled by solvent-assisted flavor evaporation. Eight odorants predicted to contribute to Wagyu beef aroma were compared between Japanese Black cattle and Holstein cattle using a stable isotope dilution assay with GC-tandem quadrupole mass spectrometry. By correlating the sensory evaluation values of retronasal aroma, γ-hexalactone, γ-d2ecalactone, and γ-undecalactone showed a high correlation with the Wagyu beef aroma. Metabolomics data revealed a high correlation between the amounts of odorants and multiple metabolites, such as glutamine, decanoic acid, lactic acid, and phosphoric acid. These results provide useful information for assessing the aroma and quality of beef.