A high cell density strategy has been used in bioethanol production to shorten the fermentation period. To reveal the molecular basis of fermentative behavior in high cell density, the profiling of the phospholipids and sterols of Saccharomyces cerevisiae during fermentation at five different pitching rates (1, 5, 10, 20, and 40 g/L) was investigated. Using LC/ESI/MS(n) technology, 148 phospholipid species were detected, of which 91 species were quantified, and using the gas chromatography-time-of-flight mass spectrometry procedure, a total of 11 sterols were quantified. Phospholipid samples from different pitching rates were discriminated into three groups using principal component analysis (1, 5 g/L, and the others). The main changes in the lipid profile of yeast cells with higher pitching rates were as follows: (a) the relative contents of phosphatidylglycerol and phosphatidylserine were higher while phosphatidylinositol was lower compared with lower pitching rates, (b) the saturated and the relatively shorter fatty acyl chains of phospholipids decreased, and (c) the content of ergosterol was higher. These findings suggested a regulation of the property of the membrane at the situation of high cell density and a possible approach of self-protection of the yeast cells against the high density stresses.