Fermented golden pompano is a traditional food valued for its distinctive flavor profile, largely influenced by lipid oxidation. This study evaluated the role of local Bacillus subtilis SCSMX-2 strain in regulating lipid oxidation and improving the flavor profile of the fermented golden pompano. Untargeted metabolomics was used to identify 206 differential metabolites, predominantly lipids, amino acids, and peptides. Enrichment analysis revealed glycerophospholipid metabolism as a key lipid pathway. SCSMX-2 induced moderate lipid oxidation, significantly increasing free fatty acid content, especially omega-3 polyunsaturates. Characterization of 148 volatile compounds revealed a notable increase in lipid oxidation-derived flavor compounds, with 11, including seven lipid derivatives, emerging as distinctive. Correlation analysis showed that secondary lipid oxidation products, such as sn-glycero-3-phosphoethanolamine and lysophosphatidylcholine, are precursors to key flavor compounds. These findings provide a scientific basis for the targeted regulation of flavors in traditional fermented fish.