Accurately quantifying core lipid (CL) and intact polar lipid (IPL) GDGTs is essential for investigating the sources of GDGTs and their responses to climatic and environmental changes in lacustrine systems. However, systematic comparisons of the performance of different methods for extracting GDGTs (both abundance and distribution) from lake sediments remain limited. In this study, we compared two ultrasonic organic solvent extraction methods, including a stepwise gradient extraction with dichloromethane/methanol (DCM/MeOH) solvent mixtures of different polarities and a single solvent extraction with DCM<span> </span>:<span> </span>MeOH (9<span> </span>:<span> </span>1, v<span> </span>:<span> </span>v), and two modified Bligh-Dyer (BD) methods (phosphate buffer; trichloroacetic acid) for extracting CL-GDGTs and IPL-GDGTs from saline and freshwater lake sediments. The results showed that, for CL-GDGTs, stepwise gradient extraction yielded the highest recovery, whereas no significant differences were observed in the CL-derived GDGTs proxies among the different extraction methods. For IPL-GDGTs, the BD (phosphate buffer) method achieved the highest recovery for isoprenoid GDGTs (isoGDGTs), while stepwise gradient extraction was most effective for extracting branched GDGTs (brGDGTs) and archaeol from saline lake sediments. Moreover, the consistently lower relative abundance of crenarchaeol to other isoGDGTs in CLs than in IPLs for all methods suggests that crenarchaeol is primarily produced in the lake water column, whereas other isoGDGTs have a relatively greater autochthonous production within the sediments or at the water-sediment interface. In saline lake sediments, we also observed higher relatively abundance of ≥<span> </span>7-methyl brGDGTs and tetramethylated brGDGTs in IPLs than in CLs, indicating that their source bacteria are active at the water-sediment interface or in the sediments of saline lakes. These findings will provide insights for the quantitative analysis of GDGTs in lake sediments and for the study of their sources in lacustrine environments.