Lipids preserved in geological materials mainly originate from cell membrane and leaf waxes, and have the potential to infer biological sources, metabolic pathways, and environmental information. Thus,lipid-based proxies have been widely applied to reconstruct paleoenvironment and paleoecology in the Quaternary. Except the concentration and molecular composition, the carbon isotope compositions of lipids are also a type of important signal sources. For photoautotrophs, the carbon isotope compositions of lipids are mainly mediated by the carbon isotope discrimination during the photosynthesis and lipid biosynthesis processes. In contrast, the carbon isotope compositions of heterotroph derived lipids are controlled by substrates and the carbon isotope fractionation during biosynthesis. In this review, we overview the advances of applications of lipid carbon isotope ratios in lacustrine and peat deposits. In the near future, more attention is suggested to pay to instrumental techniques, such as reduce the sample amount, direct analysis the carbon isotope compositions of molecules with relatively large molecular weight (e.g. BHPs, GDGTs), and widely application of compound-specific radiocarbon isotope analysis. In addition, combination of carbon isotope ratios from multi lipids, or the application of dual carbon and hydrogen isotope ratios of lipids, will shed more information on the response of ecological processes to climate changes. Furthermore, more works are worthy to investigate the relation between biogeochemical processes and paleoclimate changes in the Quaternary.