Soybean flavor is considered to be essential for the aroma quality of fermented soybeans (FS) with Bacillus subtilis BJ3-2 (BJ3-2) at 37 °C. However, the key aroma compounds of the soybean flavor must be further elucidated. In this study, two candidate genes (sdaAA and katX) of BJ3-2 involved in the control of soybean flavor production were screened using prior multi-omics data. FS samples with BJ3-2, BJ3-2ΔsdaAA, BJ3-2ΔkatX, and BJ3-2ΔsdaAAΔkatX were analyzed by quantitative descriptive sensory analysis (QDA), gas chromatography–olfactometry–mass spectrometry (GC-O-MS), relative odor activity values (ROAV), and aroma addition experiments. The QDA revealed that the aroma profile of the soybean flavor in FS consisted of “sweaty”, “smoky”, “beany”, “roasted”, and “sweet” attributes. A total of 20 aroma-active compounds were detected, and 13 of them with ROAV > 1 were identified as key aroma compounds. Moreover, aroma addition experiments were conducted to further confirm the key aroma compounds of soybean flavor. Among them, 2-methylbutyric acid, 2,3,5-trimethylpyrazine, and guaiacol contributed higher aroma intensity values and ROAV, resulting in “sweaty”, “roasted”, and “smoky” attributes of soybean flavor in FS, respectively, while 1-octen-3-ol was associated with the “beany” attribute. These findings provide novel insights into the aroma attributes of soybean flavor in FS and a new strategy for revealing the key aroma compounds in fermented foods.