Food fermentation has been playing an important role in producing bioactive components (e.g., peptides), which exert many healthy effects. In this study, it was observed that natto possessed significantly higher angiotensin I-converting enzyme (ACE) inhibitory effect than soybean. Meanwhile, a total of 246 amino-containing compounds were identified via LC-Q-TOF-MS/MS, including amino acids, dipeptides, tripeptides, O-methyl-peptide, and biogenic amines, 187 of them were only detected in natto. Of the list, dipeptides, with ACE inhibitory abilities or potentials, were found to be the most significantly up-regulated class and positively correlated with significantly increased ACE inhibitory activity of natto. Moreover, dynamic profiling elucidated the increased dipeptides were generated from water soluble and insoluble protein via Bacillus subtilis natto fermentation. Taken together, this study enriches the chemical diversity of natto and provides an in-depth insight into the degradation mechanism of soy protein during natto fermentation, which can be extended to other functional foods.