Estuarine delta is a critical zone for a series of biogeochemical processes including greenhouse gas emissions, organic matter transport and burial. These processes are mainly mediated by microbial activities such as heterotroph, methanogenesis, and methanotroph. However, response of microbial activities in the delta to paleoenvironmental change is less constrained. In this study, we analyzed the concentrations and compositions of microbial ether lipids (branched GDGTs and isoprenoid GDGTs) in a core from the Liaohe Delta, the northeast China, to explore the response of bacteria and archaea communities to climate change since 32 ka BP. During the glacial periods, the concentrations of branched GDGTs and isoprenoid GDGTs were low possibly due to the low temperature inhibiting the growth of microorganisms. After the Last Glacial Maximum (LGM), the abundance of GDGT concentrations increased, and reached the maximum during the Bølling/Allerød (B/A) period, then decreased during the Younger Dryas (YD) and increased again during the early Holocene. This pattern indicated that the abundance of the microorganisms in the Liaohe Delta was mainly controlled by temperature since 32 ka BP. In addition to temperature, sea level fluctuation and local hydrological disturbance may also effect microbial growth in the Liaohe Delta. Significant increase in the ratio of GDGT-0 versus crenarchaeol (R_0/5) indicates that the rise of lake level provided a favorable anaerobic environment for methanogen blooming during the B/A and the early Holocene. Low lake level and strong water mixing made oxygen content increase, thus inhibited methanogen growth and further led to the decrease of the R_0/5 values in the YD, suggesting that methanogenesis in global estuaries may impact atmospheric methane content. Our results provide a means to interpret response of microbial abundance and biogeochemical processes to paleoclimate change since the Last Glacial Maximum in estuarine delta.