Owing to their higher organic matter concentrations, anaerobic conditions, and abundant microbial populations, peat deposits serve as important archives for molecular paleoclimate reconstructions. For several decades, researchers have investigated the distribution patterns and origins of lipids in peat deposits, considered their relationships with environmental factors, and established a number of molecular paleoclimate proxies. Among these, proxies for paleotemperature reconstructions include the tetraether-derived methylation index/cyclisation ratio (MBT/CBT), leaf wax deltaD values, and the branched fatty alcohol ratio (BNA_(15)). Paleohydrological proxies include the deltaD offsets between individual leaf waxes,the hopanoid fluxes, and the average aromatic ring (AAR) contents. Based on these molecular proxies, histories of paleoclimate evolution since the Late Deglaciation have been reconstructed in the East Asian monsoon regions, and the boreal region of the Northern Hemisphere. As a representative site, we outlined the progresses in molecular paleoclimate reconstructions over the last decade in the Dajiuhu peat deposit, Central China. These studies clearly prove that molecular proxies, especially those related to microbial activities, are powerful tools for paleoclimate reconstructions. However, more studies are needed to fully understand the fidelities of molecular proxies and the underlying mechanisms that associate them with the climate changes, especially through the investigations of modern processes in peatlands. Furthermore, this field still needs to develop new techniques, to identify new biomarkers,to constrain the lipid sources and proxy fidelities of lipid proxies, and to establish new proxies.