Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are important archaeal membrane lipids that widely occur in marine water columns and sediments. Based on its sensitivity to temperature, the paleotemperature index TEX₈₆ was developed and extensively studied. However, GDGTs in sediments are not only affected by their external sources, but also by internal biochemical processes. The effect of bottom water redox conditions on GDGT composition and TEX₈₆ in the surface sediments remains unclear. In this study, field investigations in the eastern China marginal seas were conducted to trace the responses of sedimentary GDGTs to bottom dissolved oxygen (DO). Our results showed that the TEX₈₆ was independent of the DO level. However, the decrease in DO was accompanied by an increase in GDGT Ring Index (RI) and relative abundance of crenarchaeol (Cren) in contrast to the decrease pattern for GDGT-0, suggesting that DO has important effects on the composition of GDGTs but shows limited impact on TEX₈₆ in the study area. These changes were probably driven by archaeal adaptation, shift of community structure and degradation of GDGTs. In addition, strong relationships between DO and RI and between DO and GDGT abundances (i.e., %GDGT-0, GDGT-0/Cren) indicate that these parameters can be used as potential redox proxies for bottom water, especially in relatively stable stratified waters. Further studies coupled with archaeal community are needed to cover more areas to constrain their applicability and driving mechanisms.