The glycerol dialkyl glycerol tetraethers (GDGTs)-based indices are increasingly used to reconstruct the paleoclimate and paleoenvironment. However, the distribution of GDGTs is controlled by both climatic and complex environmental factors, which causes significant difference in the results obtained by using multiple temperature and pH calibration formulas in the same region, especially in arid areas. Here we analyzed the composition and distribution of GDGTs in surface sediments and soils of Lake Chahannaoer. Our results indicated that isoprenoid GDGTs (isoGDGTs) were dominated by crenarchaeol and GDGT-0, and branched GDGTs (brGDGTs) were dominated by the pentamethylated brGDGTs (IIa and IIa'). The community index (CI) indicated that the brGDGTs-producing bacterial community fell within clusters cold, and redundancy analysis (RDA) showed that pH was thought to be the major influencing factor for the distributions of brGDGTs in Lake Chahannaoer. The two factors might lead to differences between the reconstruction results of various climate calibration formulas and the instrumental records. Through this work, we argue that the investigation on GDGTs' modern process should be carried out to establish a suitable climate correction formula to obtain accurate paleoclimate information.