Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) and alkenones were analyzed in sediment samples retrieved from Ocean Drilling Program Site 1241 covering the last 150000 years to understand the hydrological evolution of the eastern Pacific warm pool (EPWP). GDGT and alkenone concentrations showed higher values in marine isotope stage (MIS)-2 and MIS-6, which suggests the enhancement of primary production at glacial maxima. \( {\text{TEX}}_{86}^{\text{H}} \)- and \( U_{ 3 7^\prime }^{\text{K}} \)-derived temperature depicted different temperature evolutions. \( U_{ 3 7^\prime }^{\text{K}} \)-derived temperature was marked by small variation during the glacial–interglacial cycles, whereas \( {\text{TEX}}_{86}^{\text{H}} \)-derived temperature showed pronounced glacial–interglacial variation that was similar to Mg/Ca-derived temperature records from nearby cores in the EPWP. Given that enhanced primary production during glacial maxima suggests nutricline shoaling, unchanged \( U_{ 3 7^\prime }^{\text{K}} \) over glacial–interglacial cycles can be interpreted as the shift of alkenone production depth. \( {\text{TEX}}_{86}^{\text{H}} \) seems not to be influenced by glacial–interglacial changes in nutricline depths, recording an integrated temperature in surface and thermocline water. The shallow nutricline in the EPWP during glacial maxima most likely reflected the intense formation of Antarctic intermediate water.