Soymilk is an ideal alternative to develop functional soybean foods, and fermentation can effectively enhance the digestibility and nutritional and functional properties of soymilk. In this study, the metabolites changes of soymilk fermented by Bacillus subtilis BSNK-5 were investigated through comparative metabolomics with UHPLC-Triple-TOF-MS/MS. The metabolites were gradually enriched with the extension of fermentation time and stabilized in the fermentation anaphase. In total, 289 differential metabolites were identified as the major chemical components, and they were distributed into 14 categories, mainly involving in three types of metabolites, peptides and amino acids, lipids, and flavonoids. Moreover, the fermented soymilk at 48 h exhibited the highest abundance of metabolites. Based on KEGG analysis, 14 pathways were enriched, associated with 14 specific metabolites, and mainly related to amino acid and lipid metabolism. Thus, BSNK-5 could effectively degrade the macromolecular substances of soymilk into small molecules, synthesize small peptides, small molecular acids, quinones, and isoflavone aglycones to affect the nutritional and functional properties of fermented soymilk. The in-depth analysis of metabolites in BSNK-5-fermented soymilk provides a theoretical foundation for the development of small molecule functional foods in later stages.