Distribution of lipids morphology and evolution of lipids during soy sauce production were studied. It was found that oil bodies fused and migrated to the outside of soybean cells after steamed, and further fused to cystidiums. And the model of soybean lipids distribution in soy sauce production was presented. Acid value increased to 34.4 mg KOH/g after koji fermentation, and it gradually decreased in the following fermentation. Linoleic acid (C18:2) decreased from 59.35% to 47.75% after 30 days of moromi fermentation. The contents of fatty acids from neutral lipids and free fatty acids increased to 20.98 and 13.47 mg/g, respectively, after moromi fermentation. Fatty acid of phospholipids increased to 8.34 mg/g during koji fermentation and reduced in the prior phase of moromi fermentation. The lipids model and analysis provide new insights into improving aroma of soy sauce and extraction lipids from soy sauce residue.