Reconstructing past oceanic temperatures is critical for understanding Arctic climate evolution, particularly in regions currently undergoing rapid and unprecedented change. Hydroxylated isoprenoidal glycerol dialkyl glycerol tetraether (OH-isoGDGT)–based proxies offer potential for high-latitude temperature reconstructions, yet their non-thermal controls remain poorly understood. We evaluate OH-isoGDGT-based temperature proxies from the Kongsfjorden Trough, western Svalbard, using sediment core KH17-GPC01 spanning the past 14 kyr. By comparing multiple indices (%OH, OH^C, RI-OH, RI-OH′, and TEX_86^OH) with sedimentological and environmental datasets, we assess the influence of temperature and non-thermal factors, including terrestrial organic matter (OM) input, water-depth effects, and other environmental influences, on the proxy signals. Our results indicate that temperature is the primary control on isoGDGT and OH-isoGDGT distributions, whereas non-thermal factors exert secondary influences on some indices. Among the indices examined, RI-OH′ most consistently reflects subsurface (0–200 m) depth-integrated temperatures (T0–200m), showing reduced sensitivity to terrestrial input and hydrographic variability compared to the other indices. The RI-OH′-based reconstruction indicates subsurface warming during the last deglaciation and early Holocene, peaking between 8 and 7 cal kyr BP, followed by cooling through the middle and late Holocene. These findings provide new insights into the applicability and limitations of OH-isoGDGT-based proxies in polar glacimarine environments and support the preferential application of RI-OH′ for subsurface temperature reconstructions in high-latitude fjord–shelf systems.