To better understand the compositions and sources of glycerol dialkyl glycerol tetraethers (GDGTs) and their use as proxies in the East China Sea (ECS), we analysed GDGTs in surficial sediments from the ECS outer shelf, slope and Okinawa Trough (OT) in open marine settings between 126°E and 129°E at water depths of either <100 or > 1000 m. The GDGT-0/Cren. values (0.35 ± 0.04) and methane index (MI) (0.17 ± 0.02) were generally low, indicating a negligible contribution of methanogenic Euryarchaeota GDGTs to the open marine settings in the ECS and that isoprenoid GDGTs (isoGDGTs) were mainly derived from marine planktonic Thaumarchaeota. Comprehensive analysis of the degree of cyclisation (DC) (0.34–0.53), #ringstetra (0.53–0.94), and IIIa/IIa (0.54–3.24) indices indicated that branched GDGTs (brGDGTs) may be predominantly produced in situ, with minimal soil contribution in this setting. The TEXH86-derived sea surface temperatures (SST) were closer to the annual SST than the seasonal SST from the World Ocean Atlas (WOA) 2013. The methylation of the branched tetraethers (MBT) index correlated well with the mean annual bottom water temperature (BWT) from WOA 2013. Therefore, we propose that the MBT index from open marine settings in the ECS may reflect BWT changes in marine bottom environments.