Inoculated fermentation enables rapid fermentation of aquatic products. No studies have been conducted on the lipid profiles of inoculated fermented golden pompano (Trachinotus ovatus). In this study, a lipase-producing Bacillus subtilis with salt tolerance was screened from traditionally fermented golden pompano (TF) and used as a starter culture. Whole-genome sequencing analysis revealed it carries four CRISPR structures and two genes encoding triacylglycerol lipase. Untargeted lipidomics identified lipid molecules (833) in six major classes from B. subtilis SCSMX-2 fermented golden pompano (IF). Twenty-eight lipid molecules were upregulated in IF, including phosphatidylcholines (PCs), triacylglycerols (TAGs), and lysophosphatidylcholine. B. subtilis supplementation enhanced the production of polyenyl phosphatidylcholines and medium- and long-chain triacylglycerols. The IF rich in linoleic, docosahexaenoic acids, and eicosapentaenoic acid were primarily distributed in the sn-2 position of DHA, PC and PE. This research revealed the lipid profiles of IF, providing theoretical basis for the application of B. subtilis in the fermented fish industry.