Glycerol dialkyl glycerol tetraethers (GDGTs), membrane lipids produced by archaea and some bacteria, are widely used in paleoclimatic reconstructions due to their strong correlation with temperature. However, their application in lacustrine environments remains limited as the sources (autochthonous vs allochthonous) and environmental controls on GDGT distributions are poorly constrained. To address this, we analyzed the branched and isoprenoid GDGTs (brGDGTs and isoGDGTs) in settling particles collected by sediment traps deployed at four depths in Lake Lugu, a deep alpine lake in China. The sampling period spanned 19 months with the intervals of two to three months, allowing the assessment of seasonal and depth-dependent variations. The fluxes of brGDGTs and isoGDGTs exhibited similar spatiotemporal patterns, suggesting in situ production within the water column, likely driven by nutrient upwelling during lake overturn. By correlating the fractional abundances of GDGTs and GDGT-based proxies with high-resolution water column temperature data, we evaluate their temperature dependence. The isoGDGTs, particularly the ring index, showed the strongest correlation with temperature. Notably, the isoGDGTs-temperature relationship was most robust when compared to the mean temperature of the preceding ~20 days before trap recovery. Intriguingly, the isoGDGT distribution in deeper traps (25 m) correlated more strongly with temperatures at shallower depths (15-20 m) than with their own depth, further supporting a dominant autochthonous contribution in the settling particles. In contrast, brGDGTs displayed no significant temperature dependence. Our findings provide insights into the response of GDGTs in settling particles to water column temperature variations and highlight the potential of isoGDGT-based proxies for reconstructing temperature in lacustrine environments.